Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,501,500	A→G	83.0%	Q23Q (CAA→CAG)	intB →	predicted integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,501,500	0	A	G	83.0%	130.1 / 18.1	53	Q23Q (CAA→CAG)	intB	predicted integrase
Reads supporting (aligned to +/- strand):  ref base A (2/7);  new base G (19/25);  total (21/32)
Fisher's exact test for biased strand distribution p-value = 2.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-01

CATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGT  >  W3110S.gb/4501435‑4501553                                                                  |                                                      cATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCaaaa                                                     <  1:2747933/68‑1 (MQ=255) cATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCaaaa                                                     <  1:1783452/68‑1 (MQ=255)  aTCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCaaaa                                                     <  1:1554508/67‑1 (MQ=255)     tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc                                                >  1:2627235/1‑69 (MQ=255)     tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc                                                >  1:1488589/1‑69 (MQ=255)     tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc                                                >  1:1871793/1‑69 (MQ=255)      gCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATg                                                 >  1:129241/1‑67 (MQ=255)      gCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATg                                                 >  1:1284730/1‑67 (MQ=255)      gCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCt                                               >  1:170948/1‑69 (MQ=255)       cTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCt                                               >  1:2489424/1‑68 (MQ=255)             catccaAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaaa                                                    <  1:2064417/57‑1 (MQ=255)                 cataTGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTgggg                                    <  1:2589894/66‑1 (MQ=255)                 caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTgggg                                    >  1:1811551/1‑69 (MQ=255)                 caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTgggg                                    >  1:3545836/1‑69 (MQ=255)                    aTGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTgg                                             <  1:1576625/57‑1 (MQ=255)                     tGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTg                                              >  1:887071/1‑55 (MQ=255)                     tGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTa                                >  1:634852/1‑69 (MQ=255)                          cTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCt                            >  1:3103309/1‑68 (MQ=255)                          cTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTg                           <  1:1782824/69‑1 (MQ=255)                            aaGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGa                          <  1:1623082/68‑1 (MQ=255)                             aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt                                                  <  1:1639918/43‑1 (MQ=255)                             aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt                                                  <  1:466796/43‑1 (MQ=255)                             aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt                                                  <  1:2255598/43‑1 (MQ=255)                             aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt                                                  <  1:2272820/43‑1 (MQ=255)                             aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt                                                  <  1:2310906/43‑1 (MQ=255)                             aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt                                                  <  1:483764/43‑1 (MQ=255)                               tACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt                       <  1:1412241/68‑1 (MQ=255)                               tACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt                       <  1:2026919/68‑1 (MQ=255)                               tACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAAt                       <  1:874532/68‑1 (MQ=255)                                aCTGGCTTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc                                                <  1:1419589/42‑1 (MQ=38)                                aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc                                                <  1:1400220/42‑1 (MQ=255)                                aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGc                                                <  1:3260493/42‑1 (MQ=255)                                aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATca                     <  1:3015882/69‑1 (MQ=255)                                aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATca                     <  1:428766/69‑1 (MQ=255)                                aCTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATca                     <  1:3438136/69‑1 (MQ=255)                                 cTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATca                     >  1:1454209/1‑68 (MQ=255)                                 cTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcac                    <  1:3603470/69‑1 (MQ=255)                                   ggCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt                                                  <  1:2383315/37‑1 (MQ=255)                                   ggCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAAt                                                  <  1:2235682/37‑1 (MQ=255)                                    gCGTTTGCAGTACCGTTATGAGGGAAAGCaaaaaa                                                   <  1:2662226/35‑1 (MQ=255)                                    gCGTTTGCAGTACCGTTATGAGGGAAAGCaaaaaa                                                   <  1:2344290/35‑1 (MQ=255)                                      gTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACt                 <  1:1824102/67‑1 (MQ=255)                                      gTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACt                 <  1:3189260/67‑1 (MQ=255)                                        ttGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg             <  1:2105824/69‑1 (MQ=255)                                        ttGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg             <  1:3521004/69‑1 (MQ=255)                                         tGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTa                                <  1:1847121/49‑1 (MQ=255)                                         tGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCgg            >  1:2939010/1‑69 (MQ=255)                                         tGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg             <  1:1831301/68‑1 (MQ=255)                                         tGCAGTACCGTTATGAGGGAAACCAGAAAATGCTGGCACTTGGGGTTTa                                <  1:467074/49‑1 (MQ=39)                                                ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt                                  <  1:3468265/40‑1 (MQ=255)                                                ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt                                  <  1:2639497/40‑1 (MQ=255)                                                ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg             >  1:2801363/1‑61 (MQ=255)                                                ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg             >  1:2283832/1‑61 (MQ=255)                                                ccGTTATGAGGAAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGAGGATGCCag     >  1:802661/1‑69 (MQ=255)                                                     aTGAGGGAAAGCAGAAAATGCTGGCACTTGTGGTTTATCCTGAAATCACACTAGCGGATGCCag     <  1:3270027/64‑1 (MQ=255)                                                            aaaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGt  >  1:3543800/1‑60 (MQ=255)                                                            aaaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGt  >  1:576973/1‑60 (MQ=255)                                                            aaaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGt  >  1:1428913/1‑60 (MQ=255)                                                            aaaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGt  >  1:801805/1‑60 (MQ=255)                                                                  |                                                      CATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGT  >  W3110S.gb/4501435‑4501553

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑