Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,440,918	T→C	T38A (ACT→GCT)	rpoA ←	RNA polymerase, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,440,918	0	T	C	100.0%	187.7 / NA	49	T38A (ACT→GCT)	rpoA	RNA polymerase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (28/21);  total (28/21)

GATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTT  >  NC_000913/3440787‑3441042                                                                                                                                    |                                                                                                                             gATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCa                                                                                                                       <  2:194054/139‑1 (MQ=255)      ccAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGcc                                                                                                                  >  2:273841/1‑139 (MQ=255)       cAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCa                                                                                                                 <  1:273841/139‑1 (MQ=255)            tatCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGctc                                                                                                            >  1:183584/1‑139 (MQ=255)               cTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTaa                                                                                                         >  1:985802/1‑139 (MQ=255)                  ccTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAgg                                                                                                      >  1:631287/1‑139 (MQ=255)                            ttcttTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTc                                                                                            >  2:21293/1‑139 (MQ=255)                                               tGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAAc                                                                         <  1:84196/139‑1 (MQ=255)                                                   gtaCACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCAc                                                                     >  1:1334479/1‑139 (MQ=255)                                                   gtaCACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCAc                                                                     >  1:55768/1‑139 (MQ=255)                                                   gtaCACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCAACTTGGCGTGCGTCGAACTCAc                                                                     >  1:885964/1‑139 (MQ=255)                                                         cATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAggg                                                                                              >  2:172134/1‑108 (MQ=255)                                                         cATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAggg                                                                                              <  1:172134/108‑1 (MQ=255)                                                          aTCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCg                                                              >  2:518802/1‑139 (MQ=255)                                                           tCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCa                                                                                                                 <  1:1443348/87‑1 (MQ=255)                                                           tCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCa                                                                                                                 >  2:1443348/1‑87 (MQ=255)                                                           tCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGa                                                             >  1:798322/1‑139 (MQ=255)                                                              aTCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCAc                                                                     <  2:698921/128‑1 (MQ=255)                                                              aTCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCAc                                                                     >  1:698921/1‑128 (MQ=255)                                                              aTCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGatat                                                          >  2:813103/1‑139 (MQ=255)                                                                     ccTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGcc                                                                                                                  >  1:548036/1‑76 (MQ=255)                                                                     ccTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGcc                                                                                                                  <  2:548036/76‑1 (MQ=255)                                                                      cTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAgg                                                  <  1:21293/139‑1 (MQ=255)                                                                         ggTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGgc                                                                                    >  1:552540/1‑102 (MQ=255)                                                                         ggTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGgc                                                                                    <  2:552540/102‑1 (MQ=255)                                                                          gTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACACAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGcgcg                                              >  1:1123655/1‑139 (MQ=255)                                                                           tCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCgg                                             >  1:645210/1‑139 (MQ=255)                                                                           tCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCgg                                             >  2:1039462/1‑139 (MQ=255)                                                                               cgcgCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGtttt                                         >  1:1468548/1‑139 (MQ=255)                                                                               cgcgCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGtttt                                         >  1:1415610/1‑139 (MQ=255)                                                                                gcgcAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                <  1:707995/115‑1 (MQ=255)                                                                                gcgcAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCt                                                                >  2:707995/1‑115 (MQ=255)                                                                                  gcAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGa                                      <  1:518802/139‑1 (MQ=255)                                                                                       ccGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAActc                                 <  2:645210/139‑1 (MQ=255)                                                                                       ccGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAActc                                 <  2:183584/139‑1 (MQ=255)                                                                                            aTCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTCGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTca                            <  2:666452/139‑1 (MQ=255)                                                                                              cGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTcaca                          <  2:55768/139‑1 (MQ=255)                                                                                                aTGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGc                                                                                                                   <  2:1303571/48‑1 (MQ=255)                                                                                                aTGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGc                                                                                                                   >  1:1303571/1‑48 (MQ=255)                                                                                                aTGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGa                        >  2:322001/1‑139 (MQ=255)                                                                                                aTGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGa                        >  2:644286/1‑139 (MQ=255)                                                                                                    gagCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCa                                                                                                  <  1:1260233/61‑1 (MQ=255)                                                                                                    gagCAGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCa                                                                                                  >  2:1260233/1‑61 (MQ=255)                                                                                                        aGAATACGGCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCa                <  1:56863/139‑1 (MQ=255)                                                                                                               ggCGCAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTc         <  2:1468548/139‑1 (MQ=255)                                                                                                                 cgcAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCct       <  1:644286/139‑1 (MQ=255)                                                                                                                 cgcAGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCct       >  1:592939/1‑139 (MQ=255)                                                                                                                    aGTGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCctctc    >  2:554831/1‑139 (MQ=255)                                                                                                                      tGCGTTACCCAGAGCATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAATCCTGCATTGTGTCCTCTCtt  <  2:885964/139‑1 (MQ=255)                                                                                                                                    |                                                                                                                             GATTTCCAGGATATCTTCCTGAACGCCTTCTTTGGTGCTGTACTCATGTAGTACACCATCAATCTCAACCTCGGTCACCGCGCAACCCGGCATCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTT  >  NC_000913/3440787‑3441042

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑