Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	2,963,948	G→A	intergenic (‑135/+145)	U712_15285 ← / ← U712_15290	Manganese‑binding lipoprotein mntA/o‑succinylbenzoate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	2,963,948	0	G	A	98.3%	198.3 / NA	60	intergenic (‑135/+145)	U712_15285/U712_15290	Manganese‑binding lipoprotein mntA/o‑succinylbenzoate synthase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (52/7);  minor base C (0/1);  total (52/8)
Fisher's exact test for biased strand distribution p-value = 1.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTCCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCATTTATTCAAAATAGCAA  >  CP006881/2963817‑2964080                                                                                                                                     |                                                                                                                                      tctcCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTgg                                                                                                                                >  1:301914/1‑139 (MQ=255) tctcCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTgg                                                                                                                                >  7:372837/1‑139 (MQ=255)  ctcctcctcTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGt                                                                                                                                    <  5:311853/134‑1 (MQ=255)  ctcctcctcTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGt                                                                                                                                    >  6:311853/1‑134 (MQ=255)  ctcctcctcTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTgg                                                                                                                                <  2:16851/138‑1 (MQ=255)        ctctTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCAtttt                                                                                                                         >  5:95150/1‑139 (MQ=255)          ctTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACAAAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTg                                                                                                                       >  8:215722/1‑139 (MQ=255)          ctTTGCCATCAATGTCAGATTGTTTTATCTTATGTTGTCAGTTCTTAGACAGGTGACATTAAATTAGCCAAAAGCATCTATTATTTACACAGGACAAAAAGTTT‑CCCTCATGAAAAATTATCACGTATGGCCATTTTTg                                                                                                                       >  4:465558/1‑139 (MQ=255)             tGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGGCATTTTTGTc                                                                                                                     >  6:181066/1‑138 (MQ=255)                  tCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCt                                                                                                                >  5:224488/1‑138 (MQ=255)                    aaTGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGAt                                                                                                             >  2:299383/1‑139 (MQ=255)                     aTGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGATT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGAtt                                                                                                            >  4:346983/1‑139 (MQ=255)                                ttttATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATaaaaa                                                                                                  >  3:460144/1‑138 (MQ=255)                                          tgttgtCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTggg                                                                                      >  6:469306/1‑139 (MQ=255)                                          tgttgtCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTggg                                                                                      >  5:314210/1‑139 (MQ=255)                                          tgttgtCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTggg                                                                                      >  1:436800/1‑139 (MQ=255)                                               tCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTcagc                                                                                 >  5:13721/1‑139 (MQ=255)                                               tCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTcag                                                                                  >  8:75094/1‑138 (MQ=255)                                               tCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTcag                                                                                  >  8:444488/1‑138 (MQ=255)                                               tCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTcag                                                                                  >  1:458878/1‑138 (MQ=255)                                               tCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTcag                                                                                  >  8:278452/1‑138 (MQ=255)                                               tCAGTTCTTAGACATGTGACATTAAAATAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTATGGCCATTTTTGTCAAGCTGATGTACATAAAAAA‑ACCGGCTGGTTcag                                                                                  >  8:216355/1‑138 (MQ=255)                                                 aGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTcagcag                                                                               >  2:29584/1‑139 (MQ=255)                                                 aGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTcagcag                                                                               >  1:95891/1‑139 (MQ=255)                                                 aGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTcagcag                                                                               >  5:358255/1‑139 (MQ=255)                                                        aGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTc                                                                         >  1:452786/1‑138 (MQ=255)                                                             tgtgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAg                                                                                                                  <  2:193907/93‑1 (MQ=255)                                                             tgtgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAg                                                                                                                  >  1:193907/1‑93 (MQ=255)                                                             tgtgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCaacg                                                                    >  3:23760/1‑136 (MQ=255)                                                             tgtgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAAc                                                                    >  7:301558/1‑138 (MQ=255)                                                             tgtgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAAc                                                                    >  8:422576/1‑138 (MQ=255)                                                             tgtgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAAc                                                                    >  5:324661/1‑138 (MQ=255)                                                             tgtgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAAc                                                                    >  3:135111/1‑138 (MQ=255)                                                             tgtgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGAAAAATTATAAAGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCAGCTCCAAAc                                                                    >  4:108744/1‑138 (MQ=255)                                                              gtgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAAc                                                                    >  2:107598/1‑137 (MQ=255)                                                              gtgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAAc                                                                    >  1:283722/1‑137 (MQ=255)                                                               tgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAAc                                                                    >  3:304248/1‑136 (MQ=255)                                                               tgACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAAc                                                                    >  6:454364/1‑136 (MQ=255)                                                                    taaaaTTCCCCAAATCCATGTTTTATTTACCCTGCACAAAAAGTTT‑CCCACATCAAAAATTATCAGTTTTGGCAATTTTTGACACGCTTA‑TTACAAAAAAAACCCCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAggg                                                            <  8:455331/137‑1 (MQ=255)                                                                                 aaGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACg                                                >  7:37052/1‑138 (MQ=255)                                                                                      tGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCTGCTGGGTCAGCAGCCGGTCCATACGAGAAGGGATGTATTCAACGAACACt                                          >  3:176077/1‑139 (MQ=255)                                                                                      tGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACt                                          >  3:377174/1‑139 (MQ=255)                                                                                           tatttaCACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTAc                                     >  2:6090/1‑139 (MQ=255)                                                                                                     ggACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGca                           >  3:406809/1‑139 (MQ=255)                                                                                                     gcaaaaaaaGTTC‑CCCCCATCCAAAATTAACCGGTTTGCCCATTTTTTCCAACCTTATAAAAAAAAAAAA‑CCCGGCGGGGCCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGca                           <  2:1467/135‑1 (MQ=255)                                                                                                     gcaaaaaaaGTAT‑CCCTCATCAAAAATTAACACTTTGGCCCATTTTTGACAAGCTTATTAACAAAAAAAC‑CCCGGCGGGGCCAGCAGCCGGTCCAAACGAGAAGGGAGGTATTCAACGAACACTTTTACTGTAACAGca                           <  5:181066/135‑1 (MQ=255)                                                                                                     gcaCAAAAAGTTC‑CCATAAAGAAAAATTAGCAGGTTGGGCATTTTTTGTCAAGCTTATTTACAAAAAAAC‑CCCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGca                           <  2:279640/137‑1 (MQ=255)                                                                                                      gcaaaaaaTTTTCCCCTCATCAAAAATTATCAGTTTTGGCCTTTTTTGACACGCTGATTAAAAAAAAAAA‑CCCGGCTGGGGCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGca                           <  1:299383/136‑1 (MQ=255)                                                                                                      gACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGca                           >  8:246987/1‑138 (MQ=255)                                                                                                      gACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGca                           >  8:413513/1‑138 (MQ=255)                                                                                                      gACAAAAAGTTT‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGca                           >  3:65272/1‑138 (MQ=255)                                                                                                                tt‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCTGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCAtt                 >  7:233762/1‑138 (MQ=255)                                                                                                                tt‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCAttt                >  1:70966/1‑139 (MQ=255)                                                                                                                tt‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCAtt                 >  7:431344/1‑138 (MQ=255)                                                                                                                tt‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCAtt                 >  1:346432/1‑138 (MQ=255)                                                                                                                tt‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCAtt                 >  3:136164/1‑138 (MQ=255)                                                                                                                tt‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCAtt                 >  5:84611/1‑138 (MQ=255)                                                                                                                tt‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCAtt                 >  3:393881/1‑138 (MQ=255)                                                                                                                tt‑CCCTCATGCAAAATTATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCAtt                 >  1:280879/1‑138 (MQ=255)                                                                                                                                ttATCACGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCCGCCGCCGGTCCAACCGAGAAGGGATGTATTCATCGAACACTTTTCCTGTAACAGCACAGTGTCATTTATTCAAAATAGCaa  >  2:296321/1‑138 (MQ=255)                                                                                                                                     |                                                                                                                                      TCTCCTCCTCTTTGCCATCAATGTCCGATTGTTTTATCTTATGTTGTCAGTTCTTAGACATGTGACATTAAATTAGCCAAAAGCATGTTTTATTTACACAGGACAAAAAGTTT‑CCCTCATGCAAAATTATCGCGTTTGGCCATTTTTGTCAAGCTGATTTACATAAAAAA‑ACCGGCTGGGTCAGCAGCCGGTCCAAACGAGAAGGGATGTATTCAACGAACACTTTTACTGTAACAGCACAGTGTCATTTATTCAAAATAGCAA  >  CP006881/2963817‑2964080

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑