Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,740,474	C→A	24.2%	intergenic (+39/+32)	hutF → / ← PP_5037	formiminoglutamate deiminase/lipocalin family lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,740,474	0	C	A	24.2%	81.9 / 22.4	45	intergenic (+39/+32)	hutF/PP_5037	formiminoglutamate deiminase/lipocalin family lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (13/21);  new base A (8/3);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 8.08e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.24e-01

CGCGATGTGATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTC  >  NC_002947/5740328‑5740620                                                                                                                                                   |                                                                                                                                                     cgcgATGTGATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGGATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGTGCCAGCTTTTGGGCTGAGCGTATCGTGGTTGCGTTGCAGCCCTTCGCGTGCAAGccc                                                                                                                                                     <  8:48035/148‑1 (MQ=255)       gtgATGGTGAATGGGTAATGGTTGGTGCGCCAGGGGCGGCATGCCCAGGGAGATGAAAGCGTGCGGGCGTTTGCCAAGGTGTTGCGCCATCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGGTCTTGCACGCGAAg                                                                                                                                               <  8:290684/148‑1 (MQ=255)        tgATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTTCAAGCCCGCGAAgg                                                                                                                                              <  5:138802/148‑1 (MQ=255)          aTGTTGAATGGGCAAT‑GGTGGTGCGCCACGGGCGGCATTCCCAGGAAGATGAAAGCGGGCGGGCGTTTCCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑tt                                                                                                                                          <  5:287487/148‑1 (MQ=255)          aTGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGTCCGCGAAGGG‑tt                                                                                                                                          <  4:220601/149‑1 (MQ=255)          aTGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGGCTTGCACGCGAAgggc                                                                                                                                            <  5:187689/148‑2 (MQ=38)          aTGGTGAATGGGCAATGGGGGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGAGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑tt                                                                                                                                          <  8:133453/149‑1 (MQ=255)                 aTGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTgcaacgc                                                                                                                                   <  7:225684/149‑1 (MQ=255)                   gggCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTGGCAGCCCTTCGCGTGCAAGCCCGCGCAGGG‑TTgcaacgcaa                                                                                                                                 >  5:225539/1‑149 (MQ=255)                     gCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAAcc                                                                                                                               >  7:70331/1‑149 (MQ=255)                            gtggtgCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCaaaa                                                                                                                         >  8:225082/1‑148 (MQ=255)                                                  cccAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGGAGCCCATAGCGTGGCAGCCCCCGCAGGG‑TTGGCACGCCACCCCCAAAAAC‑TAAGTGGCTTTTTTATAttt                                                                                                 >  5:115818/1‑149 (MQ=255)                                                    cAGTAAGAGTAACGCGGGCGGGCTTTGCCCAAGGGGTTGCGCCATCTTTTGGGCGGCGGGTACGGGGGTTGCGTTGCAGCCGTTCGCGTGCATGCCGGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGc                                                                                               <  2:264466/149‑1 (MQ=255)                                                    cAGGAAGATGAAAGGGGGCGGGCGTTTGCCATGGTGTTGCGCCTGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGc                                                                                               <  7:3398/149‑1 (MQ=255)                                                    cAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTTCAGCCCGTCGCGGGGAACGCCGCCCAGGGTTTACAAC‑CCACCCCAAAAAAA‑GAACTGCATTTTTAATAttttg                                                                                               >  6:87131/1‑147 (MQ=255)                                                       gAAGATCAACGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGGTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGa                                                                                            <  8:98336/149‑1 (MQ=255)                                                          gATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTTCAGCCCGTAGCGTGGGAGGCCGGGAAAGG‑TTGGCAAGCCACCCCCAAAAAA‑GAAGGGGATTTTTACTATTTGGTGAtag                                                                                         >  5:314595/1‑147 (MQ=255)                                                                                  aaGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTg                                                                 <  8:70331/149‑1 (MQ=255)                                                                                    ggTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGgt                                                               <  7:225082/149‑1 (MQ=255)                                                                                      ggtTGCGCCTGCTTTTGGGCTGAGCGTACCGGGGGTGCGTTGCAGCCCTTCGGGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACGGCAAAAAAC‑TCAGTGCAGTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGgtgt                                                             <  3:233922/148‑1 (MQ=255)                                                                                            gcCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTTCAGCCCATAGCGGGGAAGCCCGCGCAGGG‑TTTCCACCCCACCCCCAAAAAC‑ACACTGCATTTTTAATATTTTCTGATAGGACCCCCCCCAGATCAAGCGGCTGGTGTAATaac                                                       >  2:58243/1‑147 (MQ=255)                                                                                              cAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCTAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATAcccc                                                     <  7:34777/149‑1 (MQ=255)                                                                                                          tGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTgg                                                                <  5:131213/126‑1 (MQ=255)                                                                                                               gTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGa                                    <  7:205084/149‑1 (MQ=255)                                                                                                                       gttgcgttgcAACCCTTCGCGGGCTTGCACGCGAAGGG‑CTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGt                            >  3:112466/1‑149 (MQ=37)                                                                                                                         tgcgtggcCGCCCGTCGCGGGCCAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAACAC‑TCAGGGCATTTTTCCTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTtc                          <  5:82668/149‑1 (MQ=255)                                                                                                                          gcgttgcAGCCCTTCGCTTGCCAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTtc                          <  5:87131/148‑1 (MQ=255)                                                                                                                           cgttgcAACCCTTCGCGGGCTTGCACGCGAAGGG‑CTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGc                                                                                               <  2:258137/78‑1 (MQ=14)                                                                                                                           cgttgcAACCCTTCGCGGGCTTGCACGCGAAGGG‑CTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGc                                                                                               >  1:258137/1‑78 (MQ=14)                                                                                                                           cggtgcAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTtctc                        <  6:314595/146‑1 (MQ=255)                                                                                                                               gcAACCCTTCGCGGGCTTGCACGCGAAGGG‑CTGCAACGCAACCCCAAAAAACATCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACg                     >  1:80638/1‑149 (MQ=38)                                                                                                                                 aGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTc                  >  5:180601/1‑149 (MQ=255)                                                                                                                                 aGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTc                  >  6:165017/1‑149 (MQ=255)                                                                                                                                  gCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTcc                 <  6:180601/149‑1 (MQ=255)                                                                                                                                   cccTTCGCGTGCAAGCCCGCGAAGGG‑TTGCCACGGAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGTCGCCCGCCACATCAAGCTGCTGGTTTAATACCCCTGATGACGCGCCATGGACAGCACGTTCTCACGATcc                 >  5:287331/1‑148 (MQ=255)                                                                                                                                   cccTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCctgctg                                                <  7:136660/117‑1 (MQ=255)                                                                                                                                   cccTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCctgctg                                                >  8:136660/1‑117 (MQ=255)                                                                                                                                     cTTCGCGGGCTTGCACGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAg              >  7:239910/1‑149 (MQ=255)                                                                                                                                     cTTCGCGGGCTTGCACGCGAAGGG‑CTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCa                       >  2:113164/1‑140 (MQ=39)                                                                                                                                     cTTCGCGGGCTTGCACGCGAAGGG‑CTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAg              >  7:94747/1‑149 (MQ=39)                                                                                                                                      ttCGCGGGCTTGCACGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAgg             >  8:251349/1‑149 (MQ=255)                                                                                                                                      ttCGCGGGCTTGCACGCGAAGGG‑CTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAgg             >  2:79380/1‑149 (MQ=39)                                                                                                                                         gcgTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagc                                >  5:21580/1‑127 (MQ=255)                                                                                                                                         gcgTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagc                                <  6:21580/127‑1 (MQ=255)                                                                                                                                              cAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAg      <  5:61145/148‑1 (MQ=255)                                                                                                                                                 gCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTc  >  7:1596/1‑149 (MQ=255)                                                                                                                                                   ccGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCa       >  6:207241/1‑142 (MQ=255)                                                                                                                                                   ccGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCa       <  5:207241/142‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                     CGCGATGTGATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGG‑TTGCAACGCAACCCCAAAAAAC‑TCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTC  >  NC_002947/5740328‑5740620

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: ‑