Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	4,501,500	A→G	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	91.8%	192.1 / 6.3	61	Q23Q (CAA→CAG)	intB	predicted integrase
Reads supporting (aligned to +/- strand):  ref base A (4/1);  new base G (30/26);  total (34/27)
Fisher's exact test for biased strand distribution p-value = 3.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

TGCATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAC  >  W3110S.gb/4501433‑4501563                                                                    |                                                                tGCATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa                                                               <  1:1426398/70‑1 (MQ=255) tGCATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa                                                               <  1:2218072/70‑1 (MQ=255) tGCATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa                                                               <  1:1487592/70‑1 (MQ=255) tGCATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa                                                               <  1:2075466/70‑1 (MQ=255) tGCATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa                                                               <  1:512724/70‑1 (MQ=255) tGCATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaa                                                               <  1:1783146/70‑1 (MQ=255)       tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaaaa                                                             >  1:2956098/1‑66 (MQ=255)       tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaaaa                                                             >  1:75114/1‑66 (MQ=255)       tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaaaa                                                             >  1:1335232/1‑66 (MQ=255)       tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCagaaaa                                                             >  1:1750340/1‑66 (MQ=255)       tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTg                                                        >  1:417786/1‑71 (MQ=255)       tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTg                                                        >  1:2076743/1‑71 (MQ=255)       tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTg                                                        >  1:1772379/1‑71 (MQ=255)         cTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTgg                                                       <  1:3478074/70‑1 (MQ=255)                   caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt                                            <  1:2061740/71‑1 (MQ=255)                   caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt                                            <  1:3601614/71‑1 (MQ=255)                   caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt                                            <  1:2081863/71‑1 (MQ=255)                   caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt                                            <  1:2162536/71‑1 (MQ=255)                   caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt                                            <  1:3621190/71‑1 (MQ=255)                   caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt                                            <  1:873426/71‑1 (MQ=255)                   caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt                                            <  1:562636/71‑1 (MQ=255)                   caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGtt                                            <  1:386978/71‑1 (MQ=255)                   caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGtt                                            >  1:1434021/1‑71 (MQ=255)                   caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGtt                                            >  1:2702891/1‑71 (MQ=255)                               aGTACCGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAAt                                 <  1:2589761/70‑1 (MQ=255)                                      gCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAg                         <  1:640784/71‑1 (MQ=255)                                      gCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAg                         <  1:3469395/71‑1 (MQ=255)                                      gCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAg                         <  1:33109/71‑1 (MQ=255)                                      gCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAg                         <  1:1159462/71‑1 (MQ=255)                                       cGTTTGCAGTAGCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAg                         <  1:1508247/70‑1 (MQ=255)                                         tttGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTgggtt                                             <  1:3440662/48‑3 (MQ=39)                                                  ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag             >  1:2584100/1‑71 (MQ=255)                                                  ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag             >  1:2777465/1‑71 (MQ=255)                                                    gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa           >  1:401255/1‑71 (MQ=255)                                                    gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa           >  1:3557128/1‑71 (MQ=255)                                                    gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa           >  1:3387092/1‑71 (MQ=255)                                                    gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa           >  1:2875304/1‑71 (MQ=255)                                                    gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa           <  1:1210507/71‑1 (MQ=255)                                                    gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa           <  1:1664647/71‑1 (MQ=255)                                                    gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa           >  1:2279229/1‑71 (MQ=255)                                                    gTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTa           >  1:179011/1‑71 (MQ=255)                                                        tGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTAt                                         <  1:2593894/37‑1 (MQ=255)                                                        tGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTAt                                         <  1:448586/37‑1 (MQ=255)                                                          aGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGc                  <  1:3090878/58‑1 (MQ=255)                                                          aGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGc                  <  1:1166893/58‑1 (MQ=255)                                                          aGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGc                  <  1:46350/58‑1 (MQ=255)                                                          aGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGc                  <  1:4115841/58‑1 (MQ=255)                                                          aGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGc                  <  1:375109/58‑1 (MQ=255)                                                           gggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTg    <  1:1752933/71‑1 (MQ=255)                                                           gggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTg    <  1:468273/71‑1 (MQ=255)                                                            ggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCa                >  1:358619/1‑58 (MQ=255)                                                            ggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCa                >  1:2756924/1‑58 (MQ=255)                                                            ggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCa                >  1:57989/1‑58 (MQ=255)                                                            ggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCa                >  1:3550295/1‑58 (MQ=255)                                                            ggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCa                >  1:3999893/1‑58 (MQ=255)                                                            ggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCa                >  1:417489/1‑58 (MQ=255)                                                            ggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGa   >  1:1948597/1‑71 (MQ=255)                                                            ggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGa   >  1:3405203/1‑71 (MQ=255)                                                            ggAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGa   >  1:1946532/1‑71 (MQ=255)                                                             gAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCa                >  1:1683902/1‑57 (MQ=255)                                                             gAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCa                >  1:2556230/1‑57 (MQ=255)                                                               aaGCAGAAAATGCTGGCACTTGGGGTTTTTCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAc  >  1:2235019/1‑69 (MQ=255)                                                               aaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGc                  >  1:610471/1‑53 (MQ=255)                                                               aaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAc  >  1:4120819/1‑69 (MQ=255)                                                               aaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAc  >  1:3518246/1‑69 (MQ=255)                                                               aaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAc  >  1:4029666/1‑69 (MQ=255)                                                               aaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAc  >  1:3769818/1‑69 (MQ=255)                                                               aaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAc  >  1:1498672/1‑69 (MQ=255)                                                               aaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAc  >  1:2108399/1‑69 (MQ=255)                                                               aaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAc  >  1:1210349/1‑69 (MQ=255)                                                               aaGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAc  >  1:2941411/1‑69 (MQ=255)                                                                    |                                                                TGCATCTGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAGTACGTCGTGAC  >  W3110S.gb/4501433‑4501563

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑