Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,544,543	G→C	18.2%	intergenic (+60/+54)	mdfA → / ← ampG	multidrug MFS transporter/muropeptide permease AmpG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,544,543	0	G	C	18.2%	113.0 / 15.3	43	intergenic (+60/+54)	mdfA/ampG	multidrug MFS transporter/muropeptide permease AmpG
Reads supporting (aligned to +/- strand):  ref base G (13/22);  new base C (4/4);  total (17/26)
Fisher's exact test for biased strand distribution p-value = 6.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGCGGGGGTGGCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTAGGC  >  NC_002947/1544398‑1544690                                                                                                                                                  |                                                                                                                                                    cggcggGGGTGGCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCttt                                                                                                                                                 <  1:1618468/150‑1 (MQ=255)    cggGGGTGGGGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTa                                                                                                                                              <  2:188262/150‑1 (MQ=255)     gggggTGGCGGGGGCATTGGTGCTGTGGCCGAGGGGCTTAGTGGTGGGGGCGCGGCCTGGGGAAGGGGCTGTAGCTCGCTAATCGGCACTGCCGGGCCCGGCCTCTACGCGGGTAAACCCGCTCCGACGAAGCGGCGCGGCCCTGTGTAg                                                                                                                                             >  2:821164/1‑150 (MQ=16)          gggCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGGGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCg                                                                                                                                        <  2:1353374/149‑1 (MQ=18)           ggCGGGGGCGTTGGCGCTGTGGCTGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCgg                                                                                                                                       <  1:821164/150‑1 (MQ=25)           ggCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGANCgg                                                                                                                                       <  2:1190526/150‑1 (MQ=255)           ggCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCgg                                                                                                                                       <  1:746518/150‑1 (MQ=255)           ggCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCgg                                                                                                                                       <  2:1593455/150‑1 (MQ=25)           ggCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGATGTTTTGCGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCgg                                                                                                                                       <  2:1483423/150‑1 (MQ=39)            ggggggggGTTGGCCTGGAGGCCGCTGTGGTTTTCTGGGGGGGCGAGGCTTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAACCCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCggg                                                                                                                                      <  2:1258385/148‑1 (MQ=255)            gCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGTCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCggg                                                                                                                                      <  1:809389/150‑1 (MQ=255)            gCGGGGGCGTTGGCGCTGTGGCCGATGTATTGTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCggg                                                                                                                                      <  1:941313/150‑1 (MQ=255)                   ggTTGGCGCGGGGGCCGCTGGGTTTTGTGGGGGGGGGGGGGCCGGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTAccc                                                                                                                               <  2:1210825/149‑1 (MQ=18)                      tGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCcgcg                                                                                                                            <  2:1138269/150‑1 (MQ=255)                             ggggcggcGGTGGTTTGGGGGGGGTGGGCGGCCGGGGGAGGGGGCTGTAGCTGGATAATCGGTATTGCCGGGGCCGGCCGCTTCGCGGGTAACCCCGATCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGc                                                                                                                     <  2:648344/148‑1 (MQ=25)                                gCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGTCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAg                                                                                                                  >  1:191462/1‑150 (MQ=255)                                    gggggtgttGTGGAGGG‑GGGTGTCCTGGGTGGGGGGCGGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAACCCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAg                                                                                                             <  2:1849166/143‑1 (MQ=21)                                       tgGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAg                                                                                                                                             <  1:502144/116‑1 (MQ=255)                                       tgGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAg                                                                                                                                             >  2:502144/1‑116 (MQ=255)                                           ttGTGGGGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATa                                                                                                       <  1:87196/150‑1 (MQ=255)                                               ggtgggggGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACaaa                                                                                                   <  1:84883/150‑1 (MQ=255)                                                gtgggtggGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAg                                                                                                  <  2:484560/150‑1 (MQ=255)                                                gggggtgggCGGCCGGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTACGCGCAGTTGCTCGCTGCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAg                                                                                                  <  2:1097166/148‑1 (MQ=37)                                                              tGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCggg                                                                                                                                      >  2:996528/1‑100 (MQ=255)                                                              tGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCggg                                                                                                                                      <  1:996528/100‑1 (MQ=255)                                                                                               gCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGTCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTccc                                                   <  2:191462/150‑1 (MQ=255)                                                                                                       tggccTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGa                                                                                                                                           >  1:487836/2‑54 (MQ=255)                                                                                                       tggccTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGa                                                                                                                                           <  2:487836/53‑1 (MQ=255)                                                                                                              ttCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAATACAAAGCTTCAGGGCCGCTCCCCCACCGAGACGTGGGCCGCCAGCCTCGTCCCCCGCCCGGCTTCCTg                                    >  2:1647611/1‑150 (MQ=14)                                                                                                                  cgGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGAtcc                                <  2:1663744/150‑3 (MQ=255)                                                                                                                   gggTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGcc                               >  2:97815/1‑150 (MQ=255)                                                                                                                      tAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTCATCGGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACt                            >  1:1279556/1‑150 (MQ=255)                                                                                                                       aaaCCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTg                           >  1:84758/1‑150 (MQ=25)                                                                                                                          cccGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGACACTGCAg                        >  2:1044576/1‑150 (MQ=255)                                                                                                                           gcacTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAgg                       >  1:833652/4‑150 (MQ=255)                                                                                                                           ccGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAgg                       >  2:64101/1‑150 (MQ=255)                                                                                                                           ccGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCAACCCCAGTCATGGCCCTCCCGGCTTCCTGATGCCACTGCAgg                       >  1:887273/1‑150 (MQ=38)                                                                                                                           ccGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAgg                       >  1:1275804/1‑150 (MQ=25)                                                                                                                                ccTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCgat                  <  1:1044576/150‑1 (MQ=255)                                                                                                                                 cTACACAGGGCCGCGCCGCTTTGTTGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCcccgcc                                              >  1:1533298/1‑121 (MQ=255)                                                                                                                                 cTACACAGGGCCGCGCCGCTTTGTTGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCcccgcc                                              <  2:1533298/121‑1 (MQ=255)                                                                                                                                 cTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCgatc                 >  2:1619857/1‑150 (MQ=255)                                                                                                                                  tACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCgatca                >  1:668395/1‑150 (MQ=255)                                                                                                                                             gcgccgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTa     >  2:1180553/1‑150 (MQ=255)                                                                                                                                                ccgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCCACTGCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTAGGc  >  1:1755137/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                    CGGCGGGGGTGGCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTAGGC  >  NC_002947/1544398‑1544690

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: ‑