Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,740,540	T→C	15.4%	intergenic (+49/+22)	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	5,740,540	0	T	C	15.4%	98.3 / 10.8	47	intergenic (+49/+22)	hutF/PP_5037	formiminoglutamate deiminase/lipocalin family lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (17/21);  new base C (4/3);  total (23/24)
Fisher's exact test for biased strand distribution p-value = 6.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.71e-01

GATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGGTGTGCGCGACA  >  NC_002947/5740392‑5740689                                                                                                                                                       |                                                                                                                                                      gATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGtt                                                                                                                                                      <  2:381008/150‑1 (MQ=255)     gTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTgcaa                                                                                                                                                  >  2:1253185/1‑150 (MQ=255)      tGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTgcaac                                                                                                                                                 <  2:1248480/150‑1 (MQ=255)          tGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTgcaacgcaa                                                                                                                                             >  2:702864/1‑150 (MQ=255)             gCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAAccc                                                                                                                                          <  2:646389/150‑1 (MQ=255)             gCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAAccc                                                                                                                                          >  2:950586/1‑150 (MQ=255)                     tggtgCGCCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAAc                                                                                                                                  >  1:1064065/1‑150 (MQ=255)                        tgCGCCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGGGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCa                                                                                                                               <  2:349713/150‑1 (MQ=255)                         gcgcCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAg                                                                                                                              <  1:950586/150‑1 (MQ=255)                         gcgcCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAg                                                                                                                              <  1:1076703/150‑1 (MQ=255)                                   cggcATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTa                                                                                                                    <  1:237807/150‑1 (MQ=255)                                    ggcATGGCCAGGAAGATTGAAGCCGGCCGGGGGTTTGCAAAGGTGTTCCGCAGCCTTTTGGGTTGAG‑GTACCCGGGGTGCCTTTCCACCCTTCCCCTGCCAAGCCCGCGAAGGTTTGAAACGCACCCCAAAAAAACTCAGTGCATTTTTa                                                                                                                    <  2:992974/150‑1 (MQ=255)                                          cccAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTg                                                                                                             >  1:1004067/1‑150 (MQ=255)                                           ccAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGc                                                                                                            >  1:596051/1‑150 (MQ=255)                                            cAGGAAGA‑TGAAGGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTgcaa                                                                                                                                                  <  2:1070106/111‑1 (MQ=255)                                            cAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTgcaa                                                                                                                                                  >  1:1070106/1‑111 (MQ=255)                                              ggAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGa                                                                                                         >  1:802086/1‑150 (MQ=255)                                                     tGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGAc                                                                                                   <  2:802086/150‑1 (MQ=255)                                                        aaGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAATGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGAcgcc                                                                                                <  1:702864/150‑1 (MQ=255)                                                         aGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTACAGCCCTACGCGGG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTCCAAGTTGCTGATCGGAcgccc                                                                                               >  1:1030243/1‑150 (MQ=255)                                                                   cgTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCaa                                                                                     <  1:102311/150‑1 (MQ=255)                                                                    gTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAg                                                                                    >  1:688647/1‑150 (MQ=255)                                                                    gTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGG‑CTTGCACGCGAAGGGCTgc                                                                                                                                                    <  1:869251/86‑1 (MQ=18)                                                                    gTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGG‑CTTGCACGCGAAGGGCTgc                                                                                                                                                    >  2:869251/1‑86 (MQ=17)                                                                           aaGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTgg                                                                             <  2:928292/150‑1 (MQ=255)                                                                                     gcCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATAccc                                                                   <  1:1253185/150‑1 (MQ=255)                                                                                       cAGCTTTTAGGATGAGCGTACCGGGGGGGCGTTGCAGCCGTTCCCGTC‑CAAGCCCGCGAATGGGGGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCct                                                                 >  2:656210/1‑150 (MQ=255)                                                                                        aGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGTAAGTTCGCCCGCCAGATCAAGCGGCTGGTGTCATACCCctg                                                                >  1:977591/1‑150 (MQ=255)                                                                                           ttttGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCctgctg                                                             >  2:577987/1‑150 (MQ=255)                                                                                            tttGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATGCCCCtgctgc                                                            <  1:495746/150‑1 (MQ=255)                                                                                             ttGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGcc                                                           <  2:1030243/150‑1 (MQ=255)                                                                                                         tACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAca                                               <  1:577987/150‑1 (MQ=255)                                                                                                                          aacccTTCGCGGG‑CTTGCACGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCt                                                    >  1:596005/3‑128 (MQ=38)                                                                                                                          aacccTTCGCGGG‑CTTGCACGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCt                                                    <  2:596005/126‑1 (MQ=38)                                                                                                                          aGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACGATGTGCTGATCGGACGCCCGCCAGAGCAAGCGGGTGGTGTCAGAGCCCTGCTGCCGCGCCCTGGAAAGCAGGTTCTCACGCTcc                              >  1:518593/1‑150 (MQ=255)                                                                                                                           acccTTCGCGGG‑CTTGCACGCGAAGGGCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagca                                            >  1:25153/2‑135 (MQ=38)                                                                                                                           acccTTCGCGGG‑CTTGCACGCGAAGGGCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagca                                            <  2:25153/134‑1 (MQ=38)                                                                                                                            cccTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCa                            >  1:1010307/1‑150 (MQ=255)                                                                                                                            cccTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCa                            >  2:901654/1‑150 (MQ=255)                                                                                                                            cccTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGATGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCa                            <  2:1004067/150‑1 (MQ=255)                                                                                                                                 ggcgTG‑CCAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCg                       <  1:217963/149‑1 (MQ=255)                                                                                                                                    gTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCa                    <  2:1064065/150‑1 (MQ=255)                                                                                                                                    gTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCa                    <  1:1276885/150‑1 (MQ=255)                                                                                                                                     tG‑CAAGCCCGCGAAGGGGTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGGCGGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCGCCCAGACCGGCAg                   >  1:90428/1‑150 (MQ=255)                                                                                                                                       gcttgcacgcgAAGGGCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAgt                  >  1:954488/8‑150 (MQ=255)                                                                                                                                           gCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCg              >  2:191916/1‑150 (MQ=255)                                                                                                                                                 gAAGGGCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCa                            >  2:448727/1‑130 (MQ=255)                                                                                                                                                 gAAGGGCTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCa                            <  1:448727/130‑1 (MQ=255)                                                                                                                                                       ttGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCTCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGGTGTGCGCGACa  >  2:592850/1‑150 (MQ=255)                                                                                                                                                       |                                                                                                                                                      GATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGA‑TGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTG‑CAAGCCCGCGAAGGGTTGCAACGCAACCCCAAAAAACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGGTGTGCGCGACA  >  NC_002947/5740392‑5740689

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