Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,478,879	T→C	V136A (GTT→GCT)	rraB →	protein inhibitor of RNase E

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,478,879	0	T	C	95.8%	237.2 / ‑0.9	71	V136A (GTT→GCT)	rraB	protein inhibitor of RNase E
Reads supporting (aligned to +/- strand):  ref base T (1/2);  new base C (31/37);  total (32/39)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TGACGTTGAGTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGTTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCAT  >  NC_000913/4478784‑4478974                                                                                                |                                                                                                tGACGTTGAGTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGc                                                                                             <  2:640243/100‑1 (MQ=255) tGACGTTGAGTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGc                                                                                             >  2:1078130/1‑100 (MQ=255)  gACGTTGAGTACGACGGATGGGTCACTTATTTTGAAGATCCTAACGGCAAAGATGGCGACGATGAAGATTTTGTCAATGAAGACGATGACGGAGCTCGcc                                                                                            <  2:476771/100‑1 (MQ=255)   aCGTTGAGTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGcc                                                                                            >  2:1303167/1‑99 (MQ=255)    cGTTGAGTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGTGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCAc                                                                                          >  2:147266/1‑100 (MQ=255)      ttGAGTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTa                                                                                        >  2:848391/1‑100 (MQ=255)      ttGAGTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTa                                                                                        >  2:1495620/1‑100 (MQ=255)      ttGAGTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTa                                                                                        <  1:384997/100‑1 (MQ=255)      ttGAGTACGACGGATGGGGCACTTACTTTGAAGATCCGAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTa                                                                                        >  2:849879/1‑100 (MQ=255)       tGAGTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTaa                                                                                       <  2:316306/100‑1 (MQ=255)          gTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTa                                                                                    <  1:796029/100‑1 (MQ=255)           tACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTaa                                                                                   >  1:473523/1‑100 (MQ=255)           tACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCCCGCCACTAATTaa                                                                                   >  2:931500/1‑100 (MQ=255)            acgacgGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGTTCGCCACTAATTAAg                                                                                  >  1:786456/1‑100 (MQ=255)             cgacgGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGc                                                                                 >  1:400361/1‑100 (MQ=255)             cgacgGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGc                                                                                 >  1:1054063/1‑100 (MQ=255)              gacgGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCg                                                                                >  2:592288/1‑100 (MQ=255)                cgGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTa                                                                              >  2:374819/1‑100 (MQ=255)                 ggATGGCGCCGTTACATTGTAGATGCTTACGCCGAAGATGGCCACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGt                                                                               <  2:958496/98‑1 (MQ=255)                  gATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAgc                                                                            >  1:946863/1‑100 (MQ=255)                    tGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAgcgc                                                                          <  1:1180905/100‑1 (MQ=255)                    tGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAgcgc                                                                          <  1:1183624/100‑1 (MQ=255)                     ggggCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCa                                                                         >  1:716349/1‑100 (MQ=255)                     ggggCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCa                                                                         <  2:1483171/100‑1 (MQ=255)                     ggggCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCa                                                                         <  1:426825/100‑1 (MQ=255)                       ggCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATc                                                                       >  2:470696/1‑100 (MQ=255)                           cttacttTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGc                                                                   <  1:1563516/100‑1 (MQ=255)                             tacttTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGccc                                                                 <  2:473522/100‑1 (MQ=255)                             tacttTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGccc                                                                 <  2:1220269/100‑1 (MQ=255)                                 ttccgatctcTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGt                                                             <  2:489062/91‑1 (MQ=255)                                 ttGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGt                                                             <  2:870462/100‑1 (MQ=255)                                 ttGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGt                                                             <  1:1490286/100‑1 (MQ=255)                                  tGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTa                                                            >  1:80978/1‑100 (MQ=255)                                  tGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTa                                                            <  1:661792/100‑1 (MQ=255)                                  tGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACAAATTAAGCGTAGCGCATCAGGCCCAGGTa                                                            <  2:1068459/100‑1 (MQ=255)                                      gATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTc                                                        >  2:259790/1‑100 (MQ=255)                                      gATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTc                                                        >  1:456398/1‑100 (MQ=255)                                        tCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCt                                                      >  1:1418094/1‑100 (MQ=255)                                        tCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCt                                                      >  2:245/1‑100 (MQ=255)                                         ccTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTg                                                     <  1:147688/100‑1 (MQ=255)                                          cTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAgatcggaa                                                    >  1:489063/1‑93 (MQ=255)                                              cGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAAcc                                                <  1:301558/100‑1 (MQ=255)                                              cGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAAcc                                                >  1:192736/1‑100 (MQ=255)                                                 cGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTgg                                             <  2:1116101/100‑1 (MQ=255)                                                   aaGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTg                                           <  2:420237/100‑1 (MQ=255)                                                        ggCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAAttt                                      >  2:425065/1‑100 (MQ=255)                                                        ggCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAAttt                                      >  2:221629/1‑100 (MQ=255)                                                         gCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCATCCTGGTGAAtt                                       <  2:1213835/98‑1 (MQ=255)                                                         gCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTg                                     <  2:400360/100‑1 (MQ=255)                                                         gCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTg                                     <  2:1556280/100‑1 (MQ=255)                                                          cgacgaTGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGt                                    <  1:1495629/100‑1 (MQ=255)                                                          cgacgaTGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGt                                    <  2:445015/100‑1 (MQ=255)                                                          cgacgaTGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGt                                    <  2:1432050/100‑1 (MQ=255)                                                             cgaTGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGc                                 <  1:778395/100‑1 (MQ=255)                                                                tGAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCg                              >  2:606329/1‑100 (MQ=255)                                                                 gAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCgg                             <  1:857493/100‑1 (MQ=255)                                                                 gAAGATTTTGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCgg                             <  1:862560/100‑1 (MQ=255)                                                                       tttGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAgg                       <  1:433536/100‑1 (MQ=255)                                                                       tttGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAgg                       <  1:390741/100‑1 (MQ=255)                                                                       tttGTCGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAgg                       <  2:1446894/100‑1 (MQ=255)                                                                           tCGATGAAGACGATGACGGAGTTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCAtt                   <  1:406170/100‑1 (MQ=255)                                                                            cGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTc                  >  2:1147967/1‑100 (MQ=255)                                                                            cGATGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTc                  >  2:1527921/1‑100 (MQ=255)                                                                              aTGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCAt                >  1:1270413/1‑100 (MQ=255)                                                                               tGAAGACGATGACGGAGTTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATg               <  2:1185983/100‑1 (MQ=255)                                                                               tGAAGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATg               <  2:716347/100‑1 (MQ=255)                                                                                  aGACGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTca            >  2:139572/1‑100 (MQ=255)                                                                                     cGATGACGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACAt         <  1:1372376/100‑1 (MQ=255)                                                                                           cGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCa   <  2:848708/100‑1 (MQ=255)                                                                                           cGGAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCa   >  2:112649/1‑100 (MQ=255)                                                                                            ggAGCTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCAt  >  2:37991/1‑100 (MQ=255)                                                                                                |                                                                                                TGACGTTGAGTACGACGGATGGGGCACTTACTTTGAAGATCCTAACGGCGAAGATGGCGACGATGAAGATTTTGTCGATGAAGACGATGACGGAGTTCGCCACTAATTAAGCGTAGCGCATCAGGCCCAGGTAGTTCCTGCAACCTGGTGAATTTGTAGCCCGGATAAGGCATTCATGTCACATCCGGCAT  >  NC_000913/4478784‑4478974

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑