Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,740,474	C→A	25.4%	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	25.4%	76.1 / 24.0	43	intergenic (+39/+32)	hutF/PP_5037	formiminoglutamate deiminase/lipocalin family lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (10/22);  new base A (7/4);  total (17/26)
Fisher's exact test for biased strand distribution p-value = 8.00e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.65e-01

CGCGATGTGATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGG  >  NC_002947/5740328‑5740622                                                                                                                                                   |                                                                                                                                                      cgcgATGTGATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGccc                                                                                                                                                      <  2:311631/148‑1 (MQ=255)     aTGTGATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGaa                                                                                                                                                 <  6:68340/149‑1 (MQ=255)     aTGTGATGGAGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGaa                                                                                                                                                 <  7:333261/149‑1 (MQ=255)          aTGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGG‑Gtt                                                                                                                                           <  2:142292/149‑1 (MQ=255)                              ggtgCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGGCTTGCACGCGAAgg‑gct                                                                                                                                           >  3:339649/1‑127 (MQ=38)                              ggtgCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGGCTTGCACGCGAAgg‑gct                                                                                                                                           <  4:339649/129‑3 (MQ=38)                                 gcgcCCGGGGCCGCATGCCCAGGAAGATGACCCCGGGCGGGCGGTTGCCAAGGGGTGCCGCCAGCGTTTGGGCGGAGCGTACCGGGGTTGCGTTGCAGCCCTGCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCa                                                                                                                    <  4:231708/149‑1 (MQ=255)                                 gcgcCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCCTTGCAGCCCTTCGCGGGGAAGCCCGCGAACG‑GGTGGAACGCCACCCCCAAAAAca                                                                                                                      >  5:379090/1‑146 (MQ=255)                                       ggggCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCAt                                                                                                              <  1:266875/149‑1 (MQ=255)                                                   ccAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTTCAGCCCTTAGCGTGCAAGCCCGCGAAGG‑GTTGGCACGCAACCCCAAAAAAATCAGTGCATTTTTTCTAtttt                                                                                                  >  2:24704/1‑148 (MQ=255)                                                   ccAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTg                                                                                                  <  8:291953/149‑1 (MQ=255)                                                   ccAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGGCTTGCACGCGAAg                                                                                                                                                <  6:177473/104‑1 (MQ=37)                                                    cAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTTGAGCCCATAGCGGGGAAGCCCGCGAAAG‑GTTTGAACGCCAACCCAAAAAAAAAAGTGGAATTTTTATAttttg                                                                                                 >  6:142546/1‑147 (MQ=255)                                                     aGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTAGCGTGGCAGCCCGGGCAGG‑GTTGGCACGCCACCCCAAAAAACGCAGGGGCTTTTTACTATTTTCt                                                                                                >  1:239005/1‑149 (MQ=255)                                                         aGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATc                                                                                            <  1:24704/149‑1 (MQ=255)                                                             gAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGGCTTGCACGCGAAg                                                                                                                                                >  3:5015/1‑94 (MQ=25)                                                             gAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGGCTTGCACGCGAAg                                                                                                                                                <  4:5015/94‑1 (MQ=25)                                                                                   tggTGTGGCGCCAGCTTTTGGGCGTAGCTTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCTAAGG‑GTTTCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTgg                                                                  <  4:11881/148‑1 (MQ=255)                                                                                     gtgtTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGGGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGgtg                                                                <  7:278520/149‑1 (MQ=255)                                                                                     gtgtTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGGCGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTAttt                                                                                                   <  1:71643/115‑1 (MQ=255)                                                                                       gtTCCGCCATCTTTTGGGCTGTGCGTACCGGGGTTGCGTTGCAGCCGTTCGCGGCCAAGCCCGCGATGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTc                                                              <  8:125227/149‑1 (MQ=255)                                                                                           cgcCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATa                                                           <  5:154796/148‑1 (MQ=255)                                                                                                  ttttGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACACAGTGCATTTTTAGTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTGATACCCctgct                                                   >  7:265776/1‑149 (MQ=255)                                                                                                       ggCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGAAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCcgc                                              <  2:239005/149‑1 (MQ=255)                                                                                                        gCTGTGCGTACGGGGGTTGCGTTCCTGCCTGTCGGGTGAATGCCGGCTATGG‑TTTCAAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGcc                                                <  5:25644/146‑1 (MQ=255)                                                                                                                       gttgcgttgcAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGt                              >  6:231423/1‑149 (MQ=255)                                                                                                                        ttgcgttgcAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagccccc                              >  8:277990/1‑144 (MQ=255)                                                                                                                           cgttgcAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTtctc                          <  5:231423/149‑1 (MQ=255)                                                                                                                            gttgcAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCa                         <  3:217784/149‑1 (MQ=255)                                                                                                                            gttcccgCCCTTCGCGTGCACGCCCGCTACGG‑GTTGAAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCa                         <  3:329459/143‑1 (MQ=255)                                                                                                                                  acccTTCGCGGGCTTGCACGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGa                                                                              >  7:154836/2‑90 (MQ=25)                                                                                                                                  acccTTCGCGGGCTTGCACGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGa                                                                              <  8:154836/89‑1 (MQ=25)                                                                                                                                    ccTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCa                 <  5:142546/149‑1 (MQ=255)                                                                                                                                     cTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGacgcccgcccgctttcatcttcctgggcatgccgcccctggcgcaccacccattgcccattcaccatcacatcg                <  7:109326‑M2/149‑75 (MQ=255)                                                                                                                                     cTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGgt                                                                 >  3:212922/1‑100 (MQ=255)                                                                                                                                     cTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGgt                                                                 <  4:212922/100‑1 (MQ=255)                                                                                                                                     cTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAg                >  3:226069/1‑149 (MQ=255)                                                                                                                                     cTTCGCGGGCTTGCACGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCCCCCTCGACAGCAGGTTCTCACGCGCCCat                >  8:67624/1‑148 (MQ=38)                                                                                                                                     cTTCGCGGGCTTGCACGCGAAGG‑GCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAg                >  3:367587/1‑149 (MQ=39)                                                                                                                                     cTTCGCGGGCTTGCACGCGAAGG‑GCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAg                >  8:294081/1‑149 (MQ=39)                                                                                                                                      ttCGCGGGCTTGCACGCCAAGG‑GTTGCAACGCAACCACAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTAATACACCTGCTGCCGCGCCCTCTACAGCAGGTTCTAACGCTCCCAgt               >  8:143951/1‑148 (MQ=255)                                                                                                                                               aaGCCCGGTATGG‑TTTGAAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAgtg      <  5:30407/149‑1 (MQ=255)                                                                                                                                               aaGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGacgcccgcccgctttcatcttcctgggcatgccgcccc                                                    >  8:139873‑M2/1‑65 (MQ=255)                                                                                                                                               aaGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGacgcccgcccgctttcatcttcctgggcatgccgcccc                                                    <  7:139873‑M2/103‑39 (MQ=255)                                                                                                                                                   ccGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGacgcccgcccgctttcatcttcctgggcatgccgcccctggcgcaccacccattgcccattcaccatcacatcgcgcacctggcgatc  >  8:109326‑M2/1‑61 (MQ=255)                                                                                                                                                   |                                                                                                                                                      CGCGATGTGATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAGCCCGCGAAGG‑GTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGG  >  NC_002947/5740328‑5740622

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: ‑