Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,292,944	T→C	intergenic (‑22/‑583)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,292,944	0	T	C	97.8%	152.2 / NA	45	intergenic (‑22/‑583)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (25/19);  minor base G (0/1);  total (25/20)
Fisher's exact test for biased strand distribution p-value = 4.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTTCAAGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGC  >  NC_000913/1292849‑1293037                                                                                                |                                                                                              gTTTCAAGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTgcg                                                                                           >  2:1545926/1‑98 (MQ=255)  tttCAAGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTgggg                                                                                          >  2:1198856/1‑100 (MQ=255)            aCATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTttgttg                                                                                <  2:645892/100‑1 (MQ=255)            aCATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTttgttg                                                                                >  2:426479/1‑100 (MQ=255)             cATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGa                                                                               >  1:818778/1‑100 (MQ=255)             cATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGa                                                                               >  1:784988/1‑100 (MQ=255)                tctcTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGt                                                                            <  2:676075/100‑1 (MQ=255)                cgatctGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGt                                                                            <  1:384263/95‑1 (MQ=255)                  tctTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGtaa                                                                          >  1:1032434/1‑100 (MQ=255)                   ctTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGtaat                                                                         <  2:818773/100‑1 (MQ=255)                    ttGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGtaata                                                                        >  1:705505/1‑100 (MQ=255)                    ttGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGtaata                                                                        >  2:34480/1‑100 (MQ=255)                      gCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGtagatcg                                                                      >  2:384263/1‑95 (MQ=255)                         tGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTAGTTTGTTGAGGTAATAATaga                                                                   >  1:520059/1‑100 (MQ=255)                          gcgcACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATagag                                                                  >  2:705537/1‑100 (MQ=255)                            gcACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGcc                                                                <  1:1434294/100‑1 (MQ=255)                                    agTACGGATGTTGTTCAGAATTTTAATTGCGTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTc                                                        <  2:1464618/100‑1 (MQ=255)                                                gttCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAATCTTAAATTCGGTtgttg                                                >  2:712685/1‑94 (MQ=255)                                                 ttCAGACTTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGTGTGGGTTGTTGAGTTAATAATATAGCCTGAAATTCAGTTTTGCAAt                                             >  2:290751/1‑98 (MQ=255)                                                 ttCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAg                                           >  1:526150/1‑100 (MQ=255)                                                  tCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGc                                          >  2:445748/1‑100 (MQ=255)                                                  tCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGc                                          >  2:421674/1‑100 (MQ=255)                                                  tCAGAATTTTAAGTGCTTCGCTCATTGCAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGc                                          >  2:337744/1‑100 (MQ=255)                                                   cAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGACTTAAATTCAGTTGTGCAATAgac                                         >  2:480796/1‑98 (MQ=255)                                                    aGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCa                                        <  1:574376/100‑1 (MQ=255)                                                     gAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTTGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAg                                       <  2:1229597/100‑1 (MQ=255)                                                          ttAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATg                                  <  1:360959/100‑1 (MQ=255)                                                           tAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGt                                 >  2:1306575/1‑100 (MQ=255)                                                            aaGTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTa                                <  1:1490218/100‑1 (MQ=255)                                                              gTGCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAAGAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAg                              <  2:1137889/100‑1 (MQ=255)                                                                gCTTCGCTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGa                            <  1:68253/100‑1 (MQ=255)                                                                      cTCATTGTAGTAATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCaa                      >  2:485431/1‑100 (MQ=255)                                                                            gtagtaATCTCAAACTTATAGTGGGGTGGTTTTTTGAGGTAATAATCGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCaaaa                    <  1:405714/96‑1 (MQ=255)                                                                            gtagtaATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGt                >  2:1346481/1‑100 (MQ=255)                                                                            gtagtaATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGt                <  2:705503/100‑1 (MQ=255)                                                                              agtaATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTc              <  1:425206/100‑1 (MQ=255)                                                                               gtaATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCt             <  1:628980/100‑1 (MQ=255)                                                                               gtaATCTCAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCt             >  2:386661/1‑100 (MQ=255)                                                                                   tctcAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTAt         >  1:1436406/1‑100 (MQ=255)                                                                                    ctcAAACTTATACTGGGGGGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGTCAGTAATGTAAGGAATTCAAAATTGTTCTTTAt         >  2:943275/1‑99 (MQ=255)                                                                                     tcAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTAttt       <  1:474237/100‑1 (MQ=255)                                                                                     tcAAACTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTAttt       <  2:796162/100‑1 (MQ=255)                                                                                      atctcTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTAtttt      <  1:304506/96‑1 (MQ=255)                                                                                         aCTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTtgtg   <  1:1027346/100‑1 (MQ=255)                                                                                          cTTATACTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTAttttagat  >  2:304506/1‑96 (MQ=255)                                                                                                |                                                                                              GTTTCAAGTGTACATTCTCTTGCCTGCGCACGAAGAGTACGGATGTTGTTCAGAATTTTAAGTGCTTCGCTCATTGTAGTAATCTCAAACTTATATTGGGGTGGTTTGTTGAGGTAATAATAGAGCCTTAAATTCAGTTGTGCAATAGCCAGGAATGTAAGGAATTCAAAATTGTTCTTTATTTTGTGC  >  NC_000913/1292849‑1293037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑