Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	3,960,789	C→G	T338R (ACA→AGA)	rho →	transcription termination factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,960,789	0	C	G	97.9%	144.5 / ‑5.2	47	T338R (ACA→AGA)	rho	transcription termination factor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base G (25/21);  minor base T (0/1);  total (25/22)
Fisher's exact test for biased strand distribution p-value = 4.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-01

GCCAACGCCCTGCATCGTCCGAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTACAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTCACGACTCAGGAAGAACTGCAGAAAATGTGGATCCTGCGCA  >  CP009273/3960647‑3960929                                                                                                                                               |                                                                                                                                             gCCAACGCCCTGCATCCTCCGAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCaa                                                                                                                                        <  2:592948/149‑1 (MQ=255)  gcAACGCCCTGCGTCGGTCGGACCGCTTTGTTTGTTCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAACATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAAc                                                                                                                                       <  2:601428/148‑1 (MQ=255)   cAACGCCCTGCATCGTCCGAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTCTCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTCTAAAGGTAGAGGAAACa                                                                                                                                      >  2:364258/1‑149 (MQ=255)    aaCGCCCTGCATCGTCCGAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGCGGACGGCAGCATGACAATTAAAGCGACCGCCCTTATCGAGTCCGGGTTTAAGACGGGCGAGGGTATCTACGAAGGGCTTAAAGGTAGAGGCAACAt                                                                                                                                     >  2:429762/1‑149 (MQ=255)    aaCGCCCTGCATCGTCCGAAACGCTTCTTTGGTGCGGCGCGTAACGTAGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACAt                                                                                                                                     >  1:475445/1‑149 (MQ=255)     aCGCGCTGCAACGTCCGAAACGCTGCGTTGGTGCTGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATg                                                                                                                                    <  1:623008/149‑1 (MQ=255)      ctcccTGCATCGTCCCAAACGCTTCTTTGGGGCGTCGCGTAACGTGTAAGAGGGCGGCAGCCTGACCATTATCGCGATGGCGCTTTTCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATgg                                                                                                                                   <  2:689590/147‑1 (MQ=255)        cccTGCATCGTCCGAAACGCTTCTTTGGTGCGGCGCGGAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGaa                                                                                                                                 <  2:552740/149‑1 (MQ=255)          cTGCATCGTCCGAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGGCGGCGCTTATCGATACCGGTTCTAAGATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACAGGGAACt                                                                                                                               >  1:64798/1‑149 (MQ=255)             cATCGTCCGAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCa                                                                                                                            <  1:127485/149‑1 (MQ=255)              aTCGTCCGAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCAc                                                                                                                           >  1:687904/1‑149 (MQ=255)               tCGTCCGAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGGTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAAGCAACATGGAACTGCAcc                                                                                                                          >  1:52908/1‑149 (MQ=255)                    cGAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAGGGTAGAGGCAACATGGAACTGCACctctct                                                                                                                     >  1:299754/1‑149 (MQ=255)                     gAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTCTAAAGGTAGAGGCAACATGGAACTGCACCtctctc                                                                                                                    >  1:409648/1‑149 (MQ=255)                         gggttcttTGGTGCGTCGCGGAACGGGGAAGAGGGCGGAAGCCTGACCAATATCGCAACAGCGATTATCGTTACCGGTAATATCCAGGACAGAGCAATCACCGCGGAGTTGAAAGGTATATGCAACATGGAACTGCACCTCTCTCGTaa                                                                                                                <  2:147256/146‑1 (MQ=255)                            ttcttTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGAt                                                                                                             >  2:150139/1‑149 (MQ=255)                             tcttTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAGGGTAGAGGCAACGTGGAACTGCGCCTCTCTCGTAAGATc                                                                                                            >  2:236922/1‑149 (MQ=255)                              cttTGGGGCGGCGCGTAACGGGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCg                                                                                                           <  2:131452/149‑1 (MQ=255)                                 tGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTg                                                                                                        >  2:209239/1‑149 (MQ=255)                                      cggcgCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAATAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGaaaaa                                                                                                   <  2:462406/149‑1 (MQ=255)                                          gcgTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGACAAAcgcg                                                                                               >  1:677649/1‑149 (MQ=255)                                                    gAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGAGACCGGTTCTAAAATGGACGAAGTTATCTACCACGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCCCTCGTAAGATCGCTGAAAAACGCAGCCTCCCGGc                                                                                     >  2:558875/1‑149 (MQ=255)                                                      agagGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAACAGCGTCTTCCCGGCTa                                                                                   >  1:644493/1‑149 (MQ=255)                                                        agGGCGGCAACCTATCCATAAGCGCAATGGCGCTTATCGATACCGGTTCGAAAAGGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATc                                                                                 <  1:470574/149‑1 (MQ=255)                                                          ggcggcAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACCTGCATGCGCTCTTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGa                                                                               >  1:422012/1‑149 (MQ=255)                                                            cggcAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCGCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGAcg                                                                             >  1:703716/1‑148 (MQ=255)                                                             cgcAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTa                                                                            <  2:311449/148‑1 (MQ=255)                                                                        cATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTg                                                                 <  1:209239/149‑1 (MQ=255)                                                                                cgACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGt                                                         <  1:426711/149‑1 (MQ=255)                                                                                       gcTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGCCTACAACCGTTCTGGGACCCGTAacgaag                                                  >  1:60604/1‑149 (MQ=255)                                                                                               aTACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTc                                          >  2:448278/1‑149 (MQ=255)                                                                                                tACCGGTTCTAAAATGGACGAAGTTCTCCACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTCa                                         <  1:141261/149‑1 (MQ=255)                                                                                                tACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTaaa                                                      <  1:125544/136‑1 (MQ=255)                                                                                                tACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTaaa                                                      >  2:125544/1‑136 (MQ=255)                                                                                                tACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGAAAGGAAAAGCTGCTCa                                         >  1:93890/1‑149 (MQ=255)                                                                                                caccgcgtCTAAAATGCACGAGGTTACCTACGAACAGTTTAAAGGGAGAGGCACCACGGAACCGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCTGTAAAGAAGAGCTGCTCa                                         <  2:475445/142‑1 (MQ=255)                                                                                                         tAAAATGGCCCAAGTTCTCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTATACCACTCTTAAAGAAGAGCTGCTCACGACTCAgg                                <  2:159804/149‑1 (MQ=255)                                                                                                         gaaaaTGGACGAAGTTATCGACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTCACGACTCAgg                                <  2:320469/148‑1 (MQ=255)                                                                                                                gACGAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTCACGACTCAGGAAGAACt                         <  1:643249/149‑1 (MQ=255)                                                                                                                   gAAGTTATCTACGAAGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAACAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTCACGACTCAGGAAGAACTGCa                      >  2:284105/1‑149 (MQ=255)                                                                                                                        caTCTACGAAGGGTTTAAAGGTAGAGGGAACATGGAACTGCACCTCTCTCGTAAGATCGCTGTAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTCATGACTCAGGAAGAACTGCAGaaaa                 <  2:505769/148‑1 (MQ=255)                                                                                                                                aaGAGTTTAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTCACGACTCAGGAAGAACTGCAGAAAATGTGGATc         <  2:46982/149‑1 (MQ=255)                                                                                                                                     tttAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTCACGACTCAGGAAGAACTGCAGAAAATGTGGATCCTgcg    >  2:472573/1‑149 (MQ=255)                                                                                                                                     tttAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTAAAGGACGCGTCGTCCCGGCTATCGACTACAACCGTTCTGGTACCCGGAAAGAAGAGCTGCTAACGAATCAGGGAGAACGGCAGAAGATGTGGATCCTgcg    >  2:553795/1‑149 (MQ=255)                                                                                                                                     tttAAAGGTAGAGGCAACATGGAACTGCACCTCCCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTCCCCGTAAAGAAGAGCTGCTCACGACTCAGGAAGAACTGCAGAAAATGTGGATCCTgcg    <  1:24626/149‑1 (MQ=255)                                                                                                                                      ttAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTCACGACTCAGGAAGAACTGCAGAAAATGTGGATCCTgcca   >  2:635187/1‑147 (MQ=255)                                                                                                                                       tAAAGGTAGAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTCATCACGACTCAGGAAGAACTGCAGAAAATGTGGATCCTGCGCa  >  1:500091/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                             GCCAACGCCCTGCATCGTCCGAAACGCTTCTTTGGTGCGGCGCGTAACGTGGAAGAGGGCGGCAGCCTGACCATTATCGCGACGGCGCTTATCGATACCGGTTCTAAAATGGACGAAGTTATCTACGAAGAGTTTAAAGGTACAGGCAACATGGAACTGCACCTCTCTCGTAAGATCGCTGAAAAACGCGTCTTCCCGGCTATCGACTACAACCGTTCTGGTACCCGTAAAGAAGAGCTGCTCACGACTCAGGAAGAACTGCAGAAAATGTGGATCCTGCGCA  >  CP009273/3960647‑3960929

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑