Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	2	147,942	C→T	P74S (CCT→TCT)	unknown →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	2	147,942	0	C	T	100.0%	79.0 / NA	30	P74S (CCT→TCT)	unknown	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/10);  total (20/10)

CCATAGTTGAAATATTGGGCTCTTTGATGAAAACATCATTTAAAGTTGGACAAGGTGATGAGGGAATAAGATTATTTTTGAAATTATGTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGATTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACCCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTACCCTAATTATTTCTTAGATACAACTAGCTTCATAAATAGAATGGAAAACTTA  >  2/147697‑148184                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   ccATAGTTGAAATATTGGGCTCTTTGATGAAAACATCATTTAAAGTTGGACAAGGTGATGAGGGAATAAGATTATTTTTGAAATTATGTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAg                                                                                                                                                                                                                                                >  1:397539/1‑250 (MQ=255) ccATAGTTGAAATATTGGGCTCTTTGATGAAAACATCATTTAAAGTTGGACAAGGTGATGAGGGAATAAGATTATTTTTGAAATTATGTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAg                                                                                                                                                                                                                                                >  1:552175/1‑250 (MQ=255)         gAAATATTGGGCTCTTTGATGAAAACATCATTTAAAGTTGGACAAGGTGATGAGGGAATAAGATTATTTTTGAAATTATGTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAgcgc                                                                                                                                                                                                                                             >  1:790113/1‑245 (MQ=255)            atatTGGGCTCTTTGATGAAAACATCATTTAAAGTTGGACAAGGTGATGAGGGAATAAGATTATTTTTGAAATTATGTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCAtatta                                                                                                                                                                                                                                    >  1:662483/1‑251 (MQ=255)             tatTGGGCTCTTTGATGAAAACATCATTTAAAGTTGGACAAGGTGATGAGGGAATAAGATTATTTTTGAAATTATGTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCAtattat                                                                                                                                                                                                                                   <  1:417914/251‑1 (MQ=255)                                                                                 aaaTTATGTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAgcgc                                                                                                                                                                                                                                             >  1:856748/1‑173 (MQ=255)                                                                                 aaaTTATGTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCAtattat                                                                                                                                                                                                                                   <  1:807560/183‑1 (MQ=255)                                                                                 aaaTTATGTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTaa                                                                                                                                                               >  1:491089/1‑251 (MQ=255)                                                                                        gTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCAtattat                                                                                                                                                                                                                                   <  1:278819/176‑1 (MQ=255)                                                                                               attattTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCAtattat                                                                                                                                                                                                                                   >  1:512116/1‑169 (MQ=255)                                                                                                                      cTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCAtattat                                                                                                                                                                                                                                   >  1:159244/1‑146 (MQ=255)                                                                                                                       tCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCAtattat                                                                                                                                                                                                                                   >  1:94131/1‑145 (MQ=255)                                                                                                                            taataGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAg                                                                                                                    >  1:148895/1‑251 (MQ=255)                                                                                                                                            taatTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTc                                                                                                                                             >  1:583978/1‑210 (MQ=255)                                                                                                                                                      gttgtGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCAtattat                                                                                                                                                                                                                                   >  1:760546/1‑114 (MQ=255)                                                                                                                                                      gttgtGCAAATATGTGAAAAAATAAAAGAGTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGta                                                                                                                                                  >  1:58929/1‑195 (MQ=255)                                                                                                                                                                                        aTTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAgcgc                                                                                                                                                                                                                                             >  1:472386/1‑70 (MQ=255)                                                                                                                                                                                             aaaTTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTAccc                                                   <  1:287361/251‑1 (MQ=255)                                                                                                                                                                                               aTTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACat                                                                                                                                                                                                        <  1:84300/100‑1 (MQ=255)                                                                                                                                                                                                  aGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTaaa                                                               <  1:65738/234‑1 (MQ=255)                                                                                                                                                                                                    gtgtAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATattatt                                                                                                                                                                                                                                  <  1:531478/69‑1 (MQ=255)                                                                                                                                                                                                    gtgtAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTACCCTAattat                                            >  1:668547/1‑251 (MQ=255)                                                                                                                                                                                                      gtAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTc                                                                                                                                             <  1:644944/152‑1 (MQ=255)                                                                                                                                                                                                                       aaGCGTTAGTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTACCCTAATTATTTCTTAGATACAACTAg                           >  1:54695/1‑249 (MQ=255)                                                                                                                                                                                                                               gTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTAccc                                                   <  1:416588/217‑1 (MQ=255)                                                                                                                                                                                                                               gTGCTATTGATGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTACCCTAATTATTTCTTAGATACAACTAGCTTCATAAAt                 >  1:414681/1‑251 (MQ=255)                                                                                                                                                                                                                                        aTGTAGAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTACCCTAATTATTTCTTAGATACAACTAGCTTCATAAATAGAATGGaa        >  1:472192/1‑251 (MQ=255)                                                                                                                                                                                                                                             gAACATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTACCCTAATTATTTCTTAGATACAACTAGCTTCATAAATAGAATGGAAAAc     >  1:727364/1‑249 (MQ=255)                                                                                                                                                                                                                                                cATAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTACCCTAATTATTTCTTAGATACAACTAGCTTCATAAATAGAATGGAAAACTTa  >  1:483265/1‑249 (MQ=255)                                                                                                                                                                                                                                                  tAACTCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTACCCTAATTATTTCTTAGATACAACTAGCTTCATAAATAGAATGGAAAAc     <  1:522371/244‑1 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                   CCATAGTTGAAATATTGGGCTCTTTGATGAAAACATCATTTAAAGTTGGACAAGGTGATGAGGGAATAAGATTATTTTTGAAATTATGTAGTGCATTATTTTCTTATCAGGAAGATACTCCAATAATAGAAGAGTTTAATAATTTTTCTGTTGTGCAAATATGTGAAAAAATAAAAGATTTAGATTCAAAATTAGGTGTAATAGATAAACTAAAAAGCGTTAGTGCTATTGATGTAGAACATAACCCTAGCGCAGCATATTATTTGTTAATATTAGATTTAAAAAAACATAATACTGAAATTAAAACTTTTAATGAGAATGAGAAATTTAAAGCTGAGCAGGTATACTCCCATTATGAACAAGATTCTTTTAAGAATGAATTTCTTGATGTGGTGCTAGTTTCGGTTGATGATGTAAACCAATTAAAAGATGCGTACCCTAATTATTTCTTAGATACAACTAGCTTCATAAATAGAATGGAAAACTTA  >  2/147697‑148184

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑