Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,544,546	T→G	18.1%	intergenic (+63/+51)	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	1,544,546	0	T	G	18.1%	68.5 / 15.8	39	intergenic (+63/+51)	mdfA/ampG	multidrug MFS transporter/muropeptide permease AmpG
Reads supporting (aligned to +/- strand):  ref base T (15/17);  new base G (3/4);  total (18/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.57e-01

GGCGGGGGTGGCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTAGGCACCC  >  NC_002947/1544399‑1544694                                                                                                                                                    |                                                                                                                                                     ggcggGGGTGGCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCttgg                                                                                                                                                    >  2:107392/1‑148 (MQ=255)       ggTGGGGGGGGCGTGGGCGCTGGGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAg                                                                                                                                              <  2:339767/150‑1 (MQ=25)        ggggCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGc                                                                                                                                             <  1:140401/148‑1 (MQ=25)          ggCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCgg                                                                                                                                           <  1:335660/150‑1 (MQ=37)           gCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTAAATTGGGCCGCGCCGCTTTGTAGGAGCggg                                                                                                                                          <  1:744114/150‑1 (MQ=255)                 gCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTAcc                                                                                                                                    <  1:85286/150‑1 (MQ=255)                          cTGTGGCCGCTGTGGTTTGTGGTGGGTGAGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCGTTGTAGGAGCGGGTTTACCCGCGAagag                                                                                                                           >  1:586164/1‑150 (MQ=255)                                          ttGTGGTGGGTGGGCGGCCTGGGGTCAGACGTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATa                                                                                                           <  1:399220/150‑1 (MQ=37)                                              ggtgggtgGGGGGACCGGGGAAGGGGCTGTAGCGCGATGATCCGTATTCTCGGGGCCGGCGTCTTCGCGGGTATGCCTGCTCTGACGCAGGGCCGTGCCGCTTGGTAGGAGCGGGTTGACCCGCGAAGAGGCCAGCACAGGCAATACaaa                                                                                                       <  2:211728/150‑1 (MQ=25)                                                    tgggCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCa                                                                                                 >  2:745055/1‑150 (MQ=255)                                                                                  aTAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGc                                                                   >  2:70502/1‑150 (MQ=255)                                                                                       ttgTATTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTa                                                                                                                                                  <  2:388173/64‑1 (MQ=14)                                                                                       ttgTATTGCCTGTGCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTa                                                                                                                                                  >  1:388173/3‑66 (MQ=14)                                                                                            ttGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTc                                                         <  1:70502/150‑1 (MQ=255)                                                                                               ccGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTccc                                                       <  2:353858/149‑1 (MQ=255)                                                                                               ccGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTccc                                                       >  1:353858/1‑149 (MQ=255)                                                                                                      cggccTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCa                                                                                   >  1:720001/1‑114 (MQ=255)                                                                                                      cggccTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCa                                                                                   <  2:720001/114‑1 (MQ=255)                                                                                                          ccctTCGCGGGTAAACCCGCTCCTAGACAGGGCCGCGCGGCTTTGTAGGGGCGGGTTCACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTc                                           <  2:798570/148‑1 (MQ=255)                                                                                                                        aCCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGACACCGGCGTCCCCCGCCCGGCTTCCTGATGACACTGCa                             >  2:1748/1‑150 (MQ=255)                                                                                                                        aCCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCa                             >  2:464923/1‑150 (MQ=25)                                                                                                                         cccGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAg                            >  2:93613/1‑150 (MQ=255)                                                                                                                          ccGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCCGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAgg                           >  2:576494/1‑150 (MQ=18)                                                                                                                          ccGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAgg                           >  2:588920/1‑150 (MQ=25)                                                                                                                              tCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCga                       <  1:588920/150‑1 (MQ=37)                                                                                                                                cTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCcgc                                                                                                                                 <  1:522810/42‑1 (MQ=255)                                                                                                                                cTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCcgc                                                                                                                                 >  2:522810/1‑42 (MQ=255)                                                                                                                                cTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGt                                                                             >  2:379529/1‑94 (MQ=255)                                                                                                                                cTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGt                                                                             <  1:379529/94‑1 (MQ=255)                                                                                                                                 tACACAGGGCCGCGGCGATTGGTAGTGGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGTTCCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCgatca                    <  1:137874/150‑1 (MQ=39)                                                                                                                                    acaGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACt                                >  2:352120/1‑135 (MQ=255)                                                                                                                                    acaGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACt                                <  1:352120/135‑1 (MQ=255)                                                                                                                                      aGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCAcc                                                               >  1:55776/1‑102 (MQ=255)                                                                                                                                      aGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCAcc                                                               <  2:55776/102‑1 (MQ=255)                                                                                                                                         gccgcgccgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGc            >  2:501953/1‑150 (MQ=255)                                                                                                                                              gccgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGa                                       <  2:33456/118‑1 (MQ=255)                                                                                                                                              gccgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGa                                       >  1:33456/1‑118 (MQ=255)                                                                                                                                                cgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGAtcgccc                                 <  1:284193/122‑6 (MQ=255)                                                                                                                                                cgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGAtcgccc                                 >  2:284193/1‑117 (MQ=255)                                                                                                                                                 gcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTAGGCAc    <  1:107392/150‑1 (MQ=255)                                                                                                                                                   tttGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTGCTGATGCCACTGCAGGGCGATCAGGATCAGCGTAGGCAccc  >  2:545543/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                     GGCGGGGGTGGCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTAGGCACCC  >  NC_002947/1544399‑1544694

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑