Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,018,260	(A)8→7	coding (315/444 nt)	fliJ →	flagellar protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,018,253	0	A	.	96.2%	219.4 / 2.6	52	coding (308/444 nt)	fliJ	flagellar protein
Reads supporting (aligned to +/- strand):  ref base A (2/0);  new base . (24/26);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 4.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

CAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGAAAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATG  >  NC_000913/2018156‑2018347                                                                                                  |                                                                                               cagTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGaaa                                                                                              <  2:1482578/100‑1 (MQ=255)      tATCCAGACGATGGAAAAAGCCATGACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCAAGaaaaaaac                                                                                         <  1:734521/100‑2 (MQ=255)            gACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGtt                                                                                  >  1:134101/1‑100 (MQ=255)             aCGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTTGCGAG‑AAAAAAACAACGttt                                                                                 <  1:1621696/100‑1 (MQ=255)             aCGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGttt                                                                                 >  1:1547740/1‑100 (MQ=255)               gCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGc                                                                               <  1:945888/100‑1 (MQ=255)                cTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCa                                                                              >  1:1402264/1‑100 (MQ=255)                cTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCa                                                                              >  1:513046/1‑100 (MQ=255)                cTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCa                                                                              >  1:1532545/1‑100 (MQ=255)                     aaaaGCCATTACTCAGCATCGCCAGCAACATAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTACAGGCCt                                                                         >  1:1593679/1‑100 (MQ=255)                      aaaGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTg                                                                        <  2:1217790/100‑1 (MQ=255)                        aGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGc                                                                      <  2:968619/100‑1 (MQ=255)                         gCCATTACTCAGCATCGCCAGCAACTTAATCAGTGTACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCa                                                                     <  2:169311/100‑1 (MQ=255)                         gCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCa                                                                     >  1:580201/1‑100 (MQ=255)                           cATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGa                                                                   >  2:822143/1‑100 (MQ=255)                              tACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGACGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGaca                                                                 <  1:194439/99‑1 (MQ=255)                               aCTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACt                                                               >  1:870150/1‑100 (MQ=255)                               aCTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGAGAGAAAAAAAA‑AACGATTGCAAGCCTGGCAGacac                                                                >  2:245057/1‑99 (MQ=255)                                 tCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGc                                                             <  2:217223/100‑1 (MQ=255)                                  cAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCa                                                            >  1:1791600/1‑100 (MQ=255)                                  cAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCa                                                            >  1:1046232/1‑100 (MQ=255)                                   aGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAg                                                           <  2:915705/100‑1 (MQ=255)                                     cATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGa                                                         >  2:1142998/1‑100 (MQ=255)                                       tCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAAc                                                       <  2:1484761/100‑1 (MQ=255)                                        cGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACg                                                      >  2:1184137/1‑100 (MQ=255)                                         gCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGAAAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACg                                                      >  2:1806842/1‑100 (MQ=255)                                          ccAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGc                                                    <  2:1244400/100‑1 (MQ=255)                                            aGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCaa                                                  <  2:993154/100‑1 (MQ=255)                                                 cTTAATCAGTGGACGCAGAAAGGTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCaa                                                  <  1:756210/95‑1 (MQ=255)                                                    aaTCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAcggc                                          >  1:1745424/1‑100 (MQ=255)                                                      tCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAcggcgg                                        <  1:1355969/100‑1 (MQ=255)                                                      tCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACAATACAGGAACGGCAATAAAcggcg                                         >  2:1529895/1‑99 (MQ=255)                                                                 aGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCa                             <  1:822138/100‑1 (MQ=255)                                                                 aGAAAGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCa                             <  2:1181356/100‑1 (MQ=255)                                                                   aaaGTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAg                            <  2:43002/99‑1 (MQ=255)                                                                      gTTGACATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGaaaa                        >  2:282941/1‑100 (MQ=255)                                                                           cATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCCGGCCTGGCAGCCACTGCAGGAACGGCACTCCAAGGCGGCACTGCTTGCAGAAAACCGcc                   >  1:975322/1‑100 (MQ=255)                                                                           cATTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCg                     >  1:549963/1‑98 (MQ=255)                                                                            aTTGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCATGGCAGACACTGCAGGACCGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCt                  >  1:1146953/1‑100 (MQ=255)                                                                             ttGCCCTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGcc                   >  1:1461228/1‑98 (MQ=255)                                                                                cccTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGAt              <  1:1467180/100‑1 (MQ=255)                                                                                 ccTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGAt              <  1:838862/99‑1 (MQ=255)                                                                                 ccTGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATc             >  1:249127/1‑100 (MQ=255)                                                                                   tGAACAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAg           <  2:1375235/100‑1 (MQ=255)                                                                                     aaCAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGaa         <  1:1500428/100‑1 (MQ=255)                                                                                     aaCAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGaa         <  2:580205/100‑1 (MQ=255)                                                                                      aCAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGaaa        <  1:236762/100‑1 (MQ=255)                                                                                      aCAGTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGaaa        <  1:1355594/100‑1 (MQ=255)                                                                                         gTTGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAg     <  1:293338/100‑1 (MQ=255)                                                                                           tGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAgat   <  2:1079080/100‑1 (MQ=255)                                                                                           tGGCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAgat   >  1:1257080/1‑100 (MQ=255)                                                                                            ggCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAgatg  >  2:1652892/1‑100 (MQ=255)                                                                                            ggCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAgatg  <  2:1046242/100‑1 (MQ=255)                                                                                            ggCGAG‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGACTCGATCAGAAAAAga    >  2:551742/1‑98 (MQ=255)                                                                                                  |                                                                                               CAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCCTGAACAGTTGGCGAGAAAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATG  >  NC_000913/2018156‑2018347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑