Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,130,198	A→T	10.4%	intergenic (‑247/+57)	gcvH‑I ← / ← PP_0990	glycine cleavage system protein H/DoxX family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,130,198	0	A	T	10.4%	163.0 / 8.4	56	intergenic (‑247/+57)	gcvH‑I/PP_0990	glycine cleavage system protein H/DoxX family protein
Reads supporting (aligned to +/- strand):  ref base A (26/24);  new base T (3/3);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.77e-01

TCAATAGATTACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGAGCAGCAAGAGCCCTGCCCAGGTCAGGTGGGTGGG  >  NC_002947/1130056‑1130347                                                                                                                                                |                                                                                                                                                       tCAATAGATTACGTAAATTTACGGAGCAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCg                                                                                                                                                 >  1:597815/1‑150 (MQ=255)         ttACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCGTCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGAt                                                                                                                                         <  1:1217970/150‑1 (MQ=255)         ttACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGAt                                                                                                                                         <  2:719932/150‑1 (MQ=255)          tACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATa                                                                                                                                        <  1:1131691/150‑1 (MQ=255)            cGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACa                                                                                                                                      >  2:468038/1‑150 (MQ=255)                              ccGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGTAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGc                                                                                                                    >  2:364856/1‑150 (MQ=255)                                gTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGa                                                                                                                  >  2:555583/1‑150 (MQ=255)                                   tttattGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGt                                                                                                               <  1:501559/150‑1 (MQ=255)                                       ttGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGGCTGGACTGGCGAGGTGCCa                                                                                                           >  2:936189/1‑150 (MQ=255)                                          tgtgGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATg                                                                                                        <  2:900916/150‑1 (MQ=255)                                              gAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCt                                                                                                    >  2:289452/1‑150 (MQ=255)                                              gAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCt                                                                                                    <  1:468038/150‑1 (MQ=255)                                                  gATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCgg                                                                                                >  1:1409246/1‑150 (MQ=255)                                                       cGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CAtc                                                                                          >  1:44124/1‑150 (MQ=255)                                                         ttACAGGTGCCTCTGAGAGGAAAACAGCGTGA‑GCATCAAACCCTCGTGCACCGACGGCGAGGAGGCTGTGTATCGATTTCGCTACGACGTAGCGAAAACGATACACGTCGTGCCTGGACTGGCGAGGTGCCAATGGCCATCGAT‑CAcctc                                                                                        >  2:877175/1‑150 (MQ=255)                                                          tACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCa                                                                                       <  2:44124/150‑1 (MQ=255)                                                                   ctctGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTcagca                                                                              >  1:697771/1‑150 (MQ=255)                                                                   ctctGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTcagca                                                                              <  2:697771/150‑1 (MQ=255)                                                                      tGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAgat                                                                           <  1:1398558/150‑1 (MQ=255)                                                                             acaaGGGTTTGATGC‑TCAAACCCTTTTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAg                                                                    >  2:962008/3‑150 (MQ=255)                                                                             aaaaGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAg                                                                    >  2:87361/1‑150 (MQ=255)                                                                              aaaGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACt                                                                                     >  1:591975/1‑132 (MQ=255)                                                                              aaaGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACt                                                                                     <  2:591975/132‑1 (MQ=255)                                                                              aaaGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGc                                                                   <  1:364856/150‑1 (MQ=255)                                                                              aaaGGGTTTCA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGc                                                                   <  2:1073324/150‑1 (MQ=255)                                                                                aGGGTTTGA‑TGCTCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCTGGTTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGa                                                                 >  1:1379611/1‑150 (MQ=255)                                                                                    tttGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAAc                                                             >  2:1335095/1‑150 (MQ=255)                                                                                    tttGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAAc                                                             >  2:869270/1‑150 (MQ=255)                                                                                      tGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAAcgc                                                           <  1:830532/150‑1 (MQ=255)                                                                                          gCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGt                                                                                                               <  1:581185/96‑1 (MQ=255)                                                                                          gCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGt                                                                                                               >  2:581185/1‑96 (MQ=255)                                                                                          gCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATg                                                                                                        <  1:218852/103‑1 (MQ=255)                                                                                          gCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATg                                                                                                        >  2:218852/1‑103 (MQ=255)                                                                                                aaCCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGcc                                                  >  2:650549/1‑150 (MQ=255)                                                                                                    cTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCgt                                              <  2:978159/150‑2 (MQ=255)                                                                                                    cTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCgg                                              <  1:869270/150‑1 (MQ=255)                                                                                                             cGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAgg                                     >  1:635068/1‑150 (MQ=255)                                                                                                               aCGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGag                                   <  1:555583/150‑1 (MQ=255)                                                                                                                 ttctaggagtCTTTATATCGTTCTCGCTATATCCTAGCGAAATCGATACATTTGGTTCCTGGACTGGCTAGGTGCCAATGGCCTTCGGT‑CATCACAGTTTCAGCATATTATCCAGCGAAAACGCGCCGGCGCTTCGGGCAACTAGGatca                                 <  2:1002265/146‑1 (MQ=255)                                                                                                                 ggCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATg                                                                                                        >  1:1285626/1‑80 (MQ=255)                                                                                                                 ggCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATg                                                                                                        <  2:1285626/80‑1 (MQ=255)                                                                                                                 ggCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGagca                                 <  2:635068/150‑1 (MQ=255)                                                                                                                  gCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGagcag                                <  1:936189/150‑1 (MQ=255)                                                                                                                          gCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGAGCAGCAAGAGcc                        <  1:289452/150‑1 (MQ=255)                                                                                                                          ccggtgtATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAAGCAGGAGCAGCAAGAGcc                        >  1:760751/4‑150 (MQ=255)                                                                                                                                tATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTg                                                                                                                           >  2:458417/1‑46 (MQ=255)                                                                                                                                tATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTg                                                                                                                           <  1:458417/46‑1 (MQ=255)                                                                                                                                tATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGAGCAGCAAGAGCCCTGccc                  >  1:862152/1‑150 (MQ=255)                                                                                                                                 aTCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCC‑ACGGTGCATCCAACGATCAGCGGCACCCCGTGGCGAAACGCGGCGGCGCCTCGGGCAACCAGGGGCAGCAAGAGCCAAGCCca                 >  1:101298/1‑150 (MQ=255)                                                                                                                                  tCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCg                                                                                                 >  1:972506/1‑70 (MQ=255)                                                                                                                                  tCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCg                                                                                                 <  2:972506/70‑1 (MQ=255)                                                                                                                                    gTTTTCGCTACGTCGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAg                                      >  1:1416252/1‑126 (MQ=255)                                                                                                                                    gTTTTCGCTACGTCGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAg                                      <  2:1416252/126‑1 (MQ=255)                                                                                                                                     ttttCGCTACGTCGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATg                                                                                                        <  2:1284791/60‑1 (MQ=255)                                                                                                                                     ttttCGCTACGTCGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATg                                                                                                        >  1:1284791/1‑60 (MQ=255)                                                                                                                                          gCTACGTCGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCATCGGGCAGCCAGAAGCAGCAATAGCCCTGCCcaggtcaggag        >  2:726883/1‑148 (MQ=255)                                                                                                                                                acgGAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGAGCAGCAAGAGCCCTGCCCAGGTCAGGtgggtggg  <  2:188723/150‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                       TCAATAGATTACGTAAATTTACGGAGAAGCCGTATTTATTGTGTGGAATGATATCGTTACAGGTGCCTCTGAGAGGAAAAGGGTTTGA‑GCATCAAACCCTTGTGCACCGACGGCGAGGAGGCTGTGTATCGTTTTCGCTACGACGTAGCGAAAACGATACATGTGGTGCCTGGACTGGCGAGGTGCCAATGGCCTTCGGT‑CATCTCACTTTCAGCAGATGATCCAGCGAAAACGCGCCGGCGCCTCGGGCAACCAGGAGCAGCAAGAGCCCTGCCCAGGTCAGGTGGGTGGG  >  NC_002947/1130056‑1130347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑