Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,304,669	3 bp→TAC	intergenic (‑235/+159)	unknown ← / ← unknown	SSU rRNA ## 16S rRNA, small subunit ribosomal RNA/Osmotically‑inducible lipoprotein OsmB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,304,669	0	A	T	92.6%	53.5 / ‑2.3	27	intergenic (‑235/+161)	unknown/unknown	SSU rRNA ## 16S rRNA, small subunit ribosomal RNA/Osmotically‑inducible lipoprotein OsmB
Reads supporting (aligned to +/- strand):  ref base A (0/2);  new base T (13/12);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 4.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	1	1,304,670	0	G	A	92.6%	48.9 / ‑3.0	27	intergenic (‑236/+160)	unknown/unknown	SSU rRNA ## 16S rRNA, small subunit ribosomal RNA/Osmotically‑inducible lipoprotein OsmB
Reads supporting (aligned to +/- strand):  ref base G (0/2);  new base A (13/12);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 4.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	1	1,304,671	0	T	C	92.6%	54.9 / 1.2	27	intergenic (‑237/+159)	unknown/unknown	SSU rRNA ## 16S rRNA, small subunit ribosomal RNA/Osmotically‑inducible lipoprotein OsmB
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (13/12);  minor base . (0/2);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 4.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

ATTAATCTATTATAAATAATATAAATAAACGAATCTTCCGGCACCTATTAAGTTCAATCTTAAAATTATTTAAAACGAATCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGTATTTACTAATT‑CTTTGCAAGAGTTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTATTTGCCCACTTGGCTTCCAATCAAACCGCCAAGTGCCGCACCAC  >  1/1304462‑1304876                                                                                                                                                                                                                 |||                                                                                                                                                                                                               attaatCTTTTATAAATAATATAAATAAACGAATCTTCCGGCACCTATTAAGTTCAATCTTAAAATTATTTAAAACGAATCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGTATTTACTAATT‑CTTTGCAAGAG‑TTTTTTACAAAAAAATTGAACtttttttccaattgctaataa                                                                                                                                                                      <  1:318855/251‑16 (MQ=17)                              cGAATCTTCCGGCACCTATTAAGTTCAATCTTAAAATCATTTAAAACGAATCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGAt                                                                                                                                         <  1:306897/251‑1 (MQ=11)                                               aTTAAGTTCAATCTTAAAATTACTTAAAACGAATCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGTATTTACTAATT‑CTTTGCAAGAG‑TTTTTTACAAAAAAATTGAACtttttttc                                                                                                                                                                                   <  1:447103/192‑3 (MQ=255)                                                     ttCAATCTTAAAATCATTTAAAACGAATCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCaaaaa                                                                                                                   <  1:803828/250‑1 (MQ=14)                                                         aTCTTAAAATCATTTAAAACGAATCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTgaga                                                                                                                                          >  1:764852/1‑223 (MQ=11)                                                                   cattTAAAACGAATCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGc                                                                                                              >  1:793014/2‑241 (MQ=14)                                                                               aTCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATg                                                                                                               <  1:205842/228‑1 (MQ=17)                                                                               aTCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAAttt                                                                                        >  1:30888/1‑251 (MQ=18)                                                                               aTCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAAttt                                                                                        >  1:43455/1‑251 (MQ=18)                                                                                              cacaGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTg                                                                         >  1:476513/1‑251 (MQ=18)                                                                                                caGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTgg                                                                        >  1:314764/1‑250 (MQ=18)                                                                                                  gTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCtt                                                                     >  1:896755/1‑251 (MQ=21)                                                                                                    ttGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTg                                                                                     <  1:550647/233‑1 (MQ=18)                                                                                                    ttGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCttt                                                                    >  1:746276/1‑250 (MQ=21)                                                                                                                   ttAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATC‑AAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAaaat                                                    <  1:68217/250‑1 (MQ=21)                                                                                                                            aaaaaaCGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTAttt                                           <  1:708186/251‑1 (MQ=25)                                                                                                                                          tGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCGCTTTTGGCTTTCCGAGTTAAGTAAAATAAATTATTTGCCCACTTGGCTTc                             <  1:532233/251‑1 (MQ=25)                                                                                                                                           gTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAaaat                                                    <  1:797658/227‑1 (MQ=25)                                                                                                                                             cTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTATTTGCCCACTTGGCTTCCaa                          >  1:107148/1‑251 (MQ=37)                                                                                                                                               ataAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTgaga                                                                                                                                          >  1:716553/1‑137 (MQ=11)                                                                                                                                               ataAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTAttt                                           <  1:867558/232‑1 (MQ=25)                                                                                                                                                     cccTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTATTTGCCCACTTGGCTTc                             <  1:806376/240‑1 (MQ=37)                                                                                                                                                     cccTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTATTTGCCCACTTGGCTTCCAATCAAACCg                  >  1:77441/1‑251 (MQ=37)                                                                                                                                                     cccTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATC‑AAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTATTTGCCCACTTGGCTTCCAATCAAACCg                  >  1:554485/1‑250 (MQ=37)                                                                                                                                                               gcgcGTCGTTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTATTTGCCCACTTGGCTTCCAATCAAACCGCCAAGTGCCg        >  1:169811/1‑251 (MQ=38)                                                                                                                                                                  cgtcgtTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTATTTGCCCACTTGGCTTCCAATCAAACCGCTAAGTGCCGcac     <  1:421433/251‑1 (MQ=38)                                                                                                                                                                     cgtTGTGCCCGCGTATTATAGGCTTTTA‑TCCTTACCTTGCAAGTACTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTATTTGCCCACTTGGCTTCCAATCAAACCGCCAAGTGCCGcaccac  <  1:198120/251‑1 (MQ=38)                                                                                                                                                                                                                 |||                                                                                                                                                                                                               ATTAATCTATTATAAATAATATAAATAAACGAATCTTCCGGCACCTATTAAGTTCAATCTTAAAATTATTTAAAACGAATCTATAAGTGCCCACACAGTTTGTATGATTGATTGTTAAAGAACAAAAAACGACGCGCTGTCTATAAAACCCTACAACGGCGCGTCGTTGTGCCCGCGTATTATAGGTATTTACTAATT‑CTTTGCAAGAGTTTTTTTAC‑AAAAAATTGAACTTTTTTATTATTTGCTCATAAACTCGCCAAATTGTGTTTTCCTTTGAGATAAAAAATTATGGAGATCAAAAAAATGCGGTCAGAAAAACGCTTGAATTTCTGACCGCACTTTTGGCTTTCCGAGTTAAGTAAAATAAATTATTTGCCCACTTGGCTTCCAATCAAACCGCCAAGTGCCGCACCAC  >  1/1304462‑1304876

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑