Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,214,757	T→C	Y571H (TAC→CAC)	rpoD →	RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,214,757	0	T	C	100.0%	133.2 / NA	38	Y571H (TAC→CAC)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (14/24);  total (14/24)

ACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCG  >  NC_000913/3214622‑3214891                                                                                                                                        |                                                                                                                                       accaccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACcaca                                                                                                                                     >  1:1117192/1‑139 (MQ=255) accaccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACcaca                                                                                                                                     >  1:262750/1‑139 (MQ=255)  ccaccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCacac                                                                                                                                    <  1:1785173/139‑1 (MQ=255)   caccCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACg                                                                                                                                   <  2:709176/139‑1 (MQ=255)    accCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCTCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGc                                                                                                                                  <  2:1137125/139‑1 (MQ=255)           aGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGgaaga                                                                                                                           <  1:1037338/139‑1 (MQ=255)           aGCTGCCGCTGGATTCTGCGACAACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGgaaga                                                                                                                           <  1:1119529/139‑1 (MQ=255)               gCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCacac                                                                                                                                    <  2:1216432/126‑1 (MQ=255)               gCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCacac                                                                                                                                    >  1:1216432/1‑126 (MQ=255)                     ggATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTaaa                                                                                                                 <  2:262750/139‑1 (MQ=255)                     ggATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTaaa                                                                                                                 <  2:1351387/139‑1 (MQ=255)                          cTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGaagaag                                                                                                                         >  1:510454/1‑126 (MQ=255)                          cTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGaagaag                                                                                                                         <  2:510454/126‑1 (MQ=255)                                 caccGAAAGCCTGTGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGtt                                                                                                     >  2:1303520/1‑139 (MQ=255)                                 caccGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGtt                                                                                                     <  2:1248308/139‑1 (MQ=255)                                     gAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTAccc                                                                                                 <  1:8161/139‑1 (MQ=255)                                         gCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                                             <  2:623304/139‑1 (MQ=255)                                         gCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                                             <  1:775646/139‑1 (MQ=255)                                             gcgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGt                                                                                         >  1:1706301/1‑139 (MQ=255)                                              tgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTa                                                                                        <  1:1303520/138‑1 (MQ=255)                                              cgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGTGTTTCGGTATCGATATGAACACTGACCacac                                                                                                                                    >  2:253270/1‑95 (MQ=255)                                              cgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGTGTTTCGGTATCGATATGAACACCGACCacac                                                                                                                                    <  1:253270/95‑1 (MQ=255)                                              cgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTa                                                                                        <  2:1766267/139‑1 (MQ=255)                                              cgtgcgGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTa                                                                                        >  2:1446223/1‑139 (MQ=255)                                                                             tGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCaa                                                         <  2:329207/139‑1 (MQ=255)                                                                                     cgTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTc                                                 >  2:397068/1‑139 (MQ=255)                                                                                            cAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAg                                          <  1:397068/139‑1 (MQ=255)                                                                                                    cTGCGTATGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTg                                  <  2:1117192/139‑1 (MQ=255)                                                                                                           tGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                                             >  1:1511169/1‑73 (MQ=255)                                                                                                           tGCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGa                                                                                             <  2:1511169/73‑1 (MQ=255)                                                                                                            gCGTTTCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGtgctg                          >  2:515921/1‑139 (MQ=255)                                                                                                                 tCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAAc                                                                                           <  1:983326/69‑1 (MQ=255)                                                                                                                 tCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAAc                                                                                           >  2:983326/1‑69 (MQ=255)                                                                                                                 tCGGTATCGATATGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCGTAg                     >  2:943629/1‑139 (MQ=255)                                                                                                                             tGAACACCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGa         <  1:1446223/139‑1 (MQ=255)                                                                                                                                 cacCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGt                              >  2:1506670/1‑114 (MQ=255)                                                                                                                                 cacCGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGt                              <  1:1506670/114‑1 (MQ=255)                                                                                                                                    cGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCcgc                                                                                               <  1:638817/46‑1 (MQ=255)                                                                                                                                    cGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCcgc                                                                                               >  2:638817/1‑46 (MQ=255)                                                                                                                                    cGACCACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCg  >  2:1618837/1‑139 (MQ=255)                                                                                                                                        |                                                                                                                                       ACCACCCTCGAGCTGCCGCTGGATTCTGCGACCACCGAAAGCCTGCGTGCGGCAACGCACGACGTGCTGGCTGGCCTGACCGCGCGTGAAGCAAAAGTTCTGCGTATGCGTTTCGGTATCGATATGAACACCGACTACACGCTGGAAGAAGTGGGTAAACAGTTCGACGTTACCCGCGAACGTATCCGTCAGATCGAAGCGAAGGCGCTGCGCAAACTGCGTCACCCGAGCCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCG  >  NC_000913/3214622‑3214891

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑