Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	176,978	A→T	10.2%	intergenic (+24/+23)	erpA → / ← yadS	iron‑sulfur cluster insertion protein/UPF0126 family inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	176,978	0	A	T	10.2%	159.5 / 8.5	49	intergenic (+24/+23)	erpA/yadS	iron‑sulfur cluster insertion protein/UPF0126 family inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (24/20);  new base T (2/3);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 6.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.46e-01

GCCTGCAATATCTGGTCGGCGGTTCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCTGTTTCCAGTGGTACGGAAAATGT  >  NC_000913/176833‑177126                                                                                                                                                  |                                                                                                                                                     gCCTGCAATATCTGGTCGGCGGTTCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTa                                                                                                                                                   >  3:382635/1‑149 (MQ=255)    tGCAATATCTGGTCGGCGGTTCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATcc                                                                                                                                                <  3:366308/149‑1 (MQ=255)       aaTATCTGGTCGGCGGTTCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACTTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAGTTTATCCGGc                                                                                                                                             <  4:617426/149‑1 (MQ=255)       aaTATCTGGTCGGCGGTTCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAGTTTATCCGGc                                                                                                                                             <  4:640419/149‑1 (MQ=255)               gTCGGCGGTTCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACAtctt                                                                                                                                      <  1:87433/148‑1 (MQ=255)                    cggTTCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTtctctc                                                                                                                                 <  1:803424/148‑1 (MQ=255)                    cggTTCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTctctct                                                                                                                                <  3:11817/149‑1 (MQ=255)                     ggTTCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCtt                                                                                                                               <  3:673852/149‑1 (MQ=255)                        tCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCa                                                                                                                             >  1:324571/1‑148 (MQ=255)                           gTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGc                                                                                                                         >  3:336557/1‑149 (MQ=255)                           gTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGc                                                                                                                         <  3:283089/149‑1 (MQ=255)                                       gAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATcc                                                                                                             >  4:449479/1‑149 (MQ=255)                                        aaGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATcc                                                                                                             >  2:150502/1‑148 (MQ=255)                                            tCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAgcg                                                                                                         >  1:27715/1‑148 (MQ=255)                                            tCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAgcg                                                                                                         >  1:385527/1‑148 (MQ=255)                                              tGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCaa                                                                                                      >  3:395116/1‑149 (MQ=255)                                                gAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCaaa                                                                                                     >  1:324280/1‑148 (MQ=255)                                                gAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCaaa                                                                                                     <  2:324571/148‑1 (MQ=255)                                                     ttCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCgg                                                                                               <  3:780989/149‑1 (MQ=255)                                                        tcGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTa                                                                                             >  2:26602/1‑148 (MQ=255)                                                         cGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCa                                                                                                                      <  1:359869/122‑1 (MQ=255)                                                         cGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCa                                                                                                                      >  2:359869/1‑122 (MQ=255)                                                             tCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTaa                                                                                       <  4:336557/149‑1 (MQ=255)                                                             tCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTaa                                                                                       <  3:489829/149‑1 (MQ=255)                                                              cATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCACATTCTCATCCAGCGCAAACGTCGGTAGCTTaa                                                                                       >  1:247718/1‑148 (MQ=255)                                                               aTCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGa                                                                                     <  4:515712/149‑1 (MQ=255)                                                                tCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGAt                                                                                    >  4:468628/1‑149 (MQ=255)                                                                 cGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGAt                                                                                    >  2:484630/1‑148 (MQ=255)                                                                            cGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATa                                                                         >  2:496547/1‑148 (MQ=255)                                                                            cGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAg                                                                        >  4:323411/1‑149 (MQ=255)                                                                                        gCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGaa                                                            <  3:449479/149‑1 (MQ=255)                                                                                        gCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGa                                                             <  1:844174/148‑1 (MQ=255)                                                                                                       gttCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACg                                              <  2:385527/148‑1 (MQ=255)                                                                                                           ttcCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCAt                                         <  4:382635/149‑1 (MQ=255)                                                                                                              cTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGcc                                      >  3:767494/1‑149 (MQ=255)                                                                                                               tttAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGccc                                     >  4:686136/1‑149 (MQ=255)                                                                                                               tttAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGccc                                     >  4:416796/1‑149 (MQ=255)                                                                                                               tttAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGccc                                     >  4:423915/1‑149 (MQ=255)                                                                                                                ttAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGccc                                     >  2:174166/1‑148 (MQ=255)                                                                                                                         aaTCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTg                            >  2:591130/1‑148 (MQ=255)                                                                                                                          aTCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTgg                           <  2:27715/148‑1 (MQ=255)                                                                                                                            cTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCt                         >  1:347121/1‑148 (MQ=255)                                                                                                                               ttgttCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGCCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCTGttt                     <  4:159766/149‑1 (MQ=255)                                                                                                                                tgttCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCACATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCTGttt                     <  2:247718/148‑1 (MQ=255)                                                                                                                                   tCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATTCTGGCTGTTTCCa                  >  1:508751/1‑148 (MQ=255)                                                                                                                                    cATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCTGTTTCCAGt                <  3:323411/149‑1 (MQ=255)                                                                                                                                     aTGTGCCGGATAGTTTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCTGTTTCCAGt                >  2:479911/1‑148 (MQ=255)                                                                                                                                        tgCCGGATAGTTTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGAcc                                           >  3:886197/1‑118 (MQ=255)                                                                                                                                        tgCCGGATAGTTTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGAcc                                           <  4:886197/118‑1 (MQ=255)                                                                                                                                              tctaaCTATCCGGCACATCTTCTCTCTTCAACGCCTATTCGCCTCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATACCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCTGTTTCCAGGGGTACGGaaa      <  4:587003/146‑1 (MQ=255)                                                                                                                                                aaaCTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCTGTTTCCAGTGGTACGGaaaa     <  1:484630/148‑1 (MQ=255)                                                                                                                                                  aCTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCTGTTTCCAGTGGTACGGaaaa     <  3:890696/146‑1 (MQ=255)                                                                                                                                                  aCTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCTGTTTCCAGTGGTACGGaaaa     >  4:890696/1‑146 (MQ=255)                                                                                                                                                  aCTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGACCATCATACTGGCTGTTTCCAGTGGTACGGaaaaaga  >  3:587003/1‑146 (MQ=255)                                                                                                                                                  |                                                                                                                                                     GCCTGCAATATCTGGTCGGCGGTTCCGTTGATTATACCGAAGGTCTGGAAGGTTCTCGTTTCATCGTGACCAACCCGAACGCGAAAAGCACCTGCGGTTGCGGTTCTTCCTTTAGTATCTAATCTGTTGTTCATGTGCCGGATAAACTATCCGGCACATCTTCTCTCTTCAACGCCCATTCTCATCCAGCGCAAACGTCGGTAGCTTAAGATGCCAACGAATAGCCGCCAGCCGAATCAATAGCGTCACGACCATGCCCATCATACTGGCTGTTTCCAGTGGTACGGAAAATGT  >  NC_000913/176833‑177126

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑