Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,297,239	T→G	K175T (AAG→ACG)	unknown ←	Phage Rha protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,297,239	0	T	G	100.0%	101.0 / NA	36	K175T (AAG→ACG)	unknown	Phage Rha protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (19/17);  total (19/17)

AGATCAACTGCCGACGAAATCATTAGAGACCTAAAAAATTTAAAAGATACTATTTTGTCCGTTGATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCTTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGACAATAAGATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGTATTCCGTTAGTGGGACGGTATATGTCTTCTCCGGTTGCGGCAGGGCAAGTTGTTTCGGCTGTTGGGCTTCGCGGTCTAAAATATCCAGCACCCAGCGGCGGAA  >  1/1297069‑1297486                                                                                                                                                                           |                                                                                                                                                                                                                                                        ttacacagttttcattttcccgctAGAGACTTAAAAAATTTAAAAGATACTATTTTGTCGGTTGATACAGACAAGGCGTTTCAAATATTTTCCCCACAGGGGGAACCGCAGCTACTGGAAAGTTTGCCCCCCCGTAAAGGGGAACTCCCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTc                                                                                                                                                                         <  1:298065/228‑1 (MQ=255)        gatttcattttaccgctAGAGACCTAAAAAATTTAAAAGATACTATTTTGTCCGTTGATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATAc                                                                                                                                                                                                                                          >  1:292320/17‑179 (MQ=255)        gatttcattttaccgctAGAGACCTAAAAAATTTAAAAGATACTATTTTGTCCGTTGATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACg                                                                                                                                                                                             >  1:648944/17‑224 (MQ=255)        gatttcattttaccgctAGAGACCTAAAAAATTTAAAAGATACTATTTTGTCCGTTGATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAg                                                                                                                                                                  >  1:696408/17‑251 (MQ=255)                                      ttttAAAAGATACTATTTTGCCCGTTGATCCAGAAAAGGCGTTTTTAAAAATTTCCCCACAGGGGGAACCGCAGCTAGTGAAAAGTTTGCCGCCCCGAAAAGCGGGACTCCCTGCTACCCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGaaaaa                                                                                                                                    <  1:106170/250‑1 (MQ=255)                                      aTTTAAAAGATACTATTTTGTCCGTTGATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGaaaaa                                                                                                                                    >  1:812229/1‑251 (MQ=255)                                                    aTTTTGTCCGTTGATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTaaa                                                                                                                      >  1:199340/1‑251 (MQ=255)                                                    aTTTTGTCCGTTGATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGCTGAATGAACAAGAAAAACACGCGTTTTTaaa                                                                                                                      >  1:299602/1‑251 (MQ=255)                                                            cGTTGATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATAc                                                                                                                                                                                                                                          >  1:519058/1‑127 (MQ=255)                                                            cGTTGATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAAtt                                                                                                              >  1:116227/1‑251 (MQ=255)                                                             gTTGATACAGACAAAGCTTTTCTAATAATTTCCCCACAGTGGGAATCGCAGCTACTGAAAAGTTTGCCGCCCCGAAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCaaaaa                                                                                                                                                                    <  1:152121/196‑1 (MQ=255)                                                                gATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACgg                                                                                                          >  1:404272/1‑251 (MQ=255)                                                                gATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACgg                                                                                                          >  1:477918/1‑251 (MQ=255)                                                                gATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTT‑TTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGt                                                                                                         <  1:891697‑M2/251‑2 (MQ=255)                                                                      gACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTaacc                                                                                                                                                                                                               >  1:681605/1‑144 (MQ=255)                                                                              gTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgg                                                                                            <  1:327782‑M2/251‑15 (MQ=255)                                                                                  cTAATAATTTCCCCACAGTGGAAATCGCAGCTACGGAAAAGTTTGCCGCCCCGTAAGGCGGGACTCCCTGCTACCCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcggggga                                                                                        >  1:808589‑M2/1‑233 (MQ=255)                                                                                        atTTCCCCACAGTGGGAACCGCAGCTACTGGAAAGTTTGCCGCCCGGTAAAGCGGGACTCCCTGCTACCCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCAc                                                                                                                                                                                              <  1:823958/143‑1 (MQ=255)                                                                                         ttttCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGc                                                                                                                                                                                      >  1:27064/1‑150 (MQ=255)                                                                                         ttttCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatc                                                                                                      <  1:652294‑M2/230‑5 (MQ=255)                                                                                             cccACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTtgaatga                                                                                                                                              >  1:581445/1‑186 (MQ=255)                                                                                             cccACAGGGGGAATCGCAGCTACGGAAAAGTTTGCCGCCCCGTAAAGGGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaac                                                                             >  1:852703‑M2/1‑222 (MQ=255)                                                                                                   gggggaaCCGCAGCTACGGGAAAGTTTGCCGCCCCGAAAAGCGGAACTCCCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataag                                                                                    >  1:367973‑M2/3‑216 (MQ=255)                                                                                                                  aCTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaact                                                         <  1:857696‑M2/250‑50 (MQ=255)                                                                                                                  aCTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaact                                                         <  1:557277‑M2/250‑50 (MQ=255)                                                                                                                  aCTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatga                                                                                                     <  1:415556‑M2/206‑6 (MQ=255)                                                                                                                                       aaaggcgggACTCCCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttgg                                   >  1:701620‑M2/5‑180 (MQ=255)                                                                                                                                              ggACTACCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTGCGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttggttcttat                            <  1:445063‑M2/251‑79 (MQ=255)                                                                                                                                                   aCCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttggttcttatcacca                       <  1:801944‑M2/251‑84 (MQ=255)                                                                                                                                                   aCCTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttggttcttatcacca                       <  1:669634‑M2/251‑84 (MQ=255)                                                                                                                                                    ccTGCTCCTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttggttcttatcaccag                      >  1:98062‑M2/1‑167 (MQ=255)                                                                                                                                                     cTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttggttcttatcaccaga                     <  1:726462‑M2/251‑86 (MQ=255)                                                                                                                                                     cTGCTACTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttggt                                  <  1:792559‑M2/238‑73 (MQ=255)                                                                                                                                                          aCTCCCGCCGATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttggttcttatcaccagaggtga                <  1:682918‑M2/251‑91 (MQ=255)                                                                                                                                                              ccgccgATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttggttcttatcaccagaggtgacgat            >  1:400355‑M2/1‑157 (MQ=255)                                                                                                                                                                 ccgATGTATCGTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttggttcttatcaccag                      <  1:508912‑M2/238‑85 (MQ=255)                                                                                                                                                                        atcgtatctAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGAAAATAAAATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGtatgacgcaatcgggggataagtgtaaactggtgttagtgggcgaaactcaccgagataatccgtatttggttcttatcaccagaggtgacgattggtcgttgc  >  1:117586‑M2/1‑147 (MQ=255)                                                                                                                                                                           |                                                                                                                                                                                                                                                        AGATCAACTGCCGACGAAATCATTAGAGACCTAAAAAATTTAAAAGATACTATTTTGTCCGTTGATACAGACAAAGCGTTTCTAATAATTTTCCCACAGTGGGAATCGCAGCTACTGGAAAGTTTGCCGCCCCGTAAAGCGGGACTACCTGCTACTCCCGCCGATGTATCTTATCTAGACAAATACAAGCCAAAGAAATAAACAACCCTAACCAACCCCAAGCCCTCCACGTGAGGGCCTTTTTATTACTCAAAAAAGGACAATAAGATGTTGAATGAACAAGAAAAACACGCGTTTTTAAATGGCAATTACGGTATTCCGTTAGTGGGACGGTATATGTCTTCTCCGGTTGCGGCAGGGCAAGTTGTTTCGGCTGTTGGGCTTCGCGGTCTAAAATATCCAGCACCCAGCGGCGGAA  >  1/1297069‑1297486

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑