Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F28 I1 R1 122 92.7 4382561 94.3% 4132755 66.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA minE 1,827,842 Δ1 bp coding (1085/2562 nt) mutS → methyl‑directed mismatch repair protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,827,8400C.98.9% 371.5 / ‑1.8 87coding (1083/2562 nt)mutSmethyl‑directed mismatch repair protein
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base . (66/20);  total (66/21)
Fisher's exact test for biased strand distribution p-value = 2.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.49e-01

CAGCCGGTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCGCCCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCG  >  minE/1827772‑1827897
                                                                    |                                                         
cAGCCGGTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCGcca                                                         <  1:4194230/71‑2 (MQ=255)
              tCAGGTCGGCGCCCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:3393077/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCCCGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:1243021/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTGTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:1332194/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCATGCGATCTGGCCCg                                          >  1:2801855/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGccc                                           >  1:2246662/1‑70 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:4068283/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:220693/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:427158/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:2341543/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:2344767/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:2454599/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:24566/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:2484201/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:2681728/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:2725912/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:956119/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:4056709/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:2852261/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:3968071/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:3211552/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:3220918/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:3705581/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:3526693/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:462681/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:1248214/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:1329220/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:1934789/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:1526640/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:1840594/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:770276/1‑71 (MQ=255)
              tCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:1687604/1‑71 (MQ=255)
              tCAGGTAGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCg                                          >  1:563110/1‑71 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCCCGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     <  1:687300/71‑1 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     >  1:4322665/1‑71 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     >  1:855238/1‑71 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     <  1:3099422/71‑1 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     >  1:1373907/1‑71 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     <  1:1382208/71‑1 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     <  1:1618849/71‑1 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     >  1:2580477/1‑71 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     <  1:675051/71‑1 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     <  1:601757/71‑1 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     <  1:2079509/71‑1 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     <  1:4301479/71‑1 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATg                                      >  1:4259570/1‑70 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATg                                      >  1:3731021/1‑70 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATg                                      >  1:1247464/1‑70 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCGGGCCCGTATgc                                     <  1:741510/71‑1 (MQ=255)
                   tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTC‑CCCACGCGATCTGGCCCGTATgc                                     <  1:417226/71‑1 (MQ=255)
                   tCGGCGACCTGGAACGTACTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                     >  1:1505560/1‑71 (MQ=255)
                       cGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCa                                 >  1:48040/1‑71 (MQ=255)
                       cGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCa                                 >  1:1121254/1‑71 (MQ=255)
                       cGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCa                                 >  1:1928643/1‑71 (MQ=255)
                       cGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCa                                 >  1:2103909/1‑71 (MQ=255)
                                   tATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGc                      >  1:981345/1‑70 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTTCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:2190664/70‑1 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAAc                   >  1:473200/1‑69 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:2063227/70‑1 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:1092751/70‑1 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:869887/70‑1 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:118392/70‑1 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:1759026/70‑1 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:572573/70‑1 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  >  1:51422/1‑70 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:481312/70‑1 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:476148/70‑1 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:2810071/70‑1 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:2148242/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:384217/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:2863938/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:859791/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:1847450/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:1903450/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:2712583/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:619351/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:58731/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:4179147/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:2037623/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:261891/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:2344300/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:345324/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:227165/1‑71 (MQ=255)
                                       cTGGCACGTCTGGCTTTACGAACTGCTCG‑CCAAGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTg                 >  1:2792569/1‑71 (MQ=255)
                                        tGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACt                  <  1:758561/69‑1 (MQ=255)
                                                      ttACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCtgcgtgcg  >  1:1958087/1‑71 (MQ=255)
                                                      ttACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCtgcgtgcg  >  1:4379684/1‑71 (MQ=255)
                                                      ttACGAACTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCtgcgtgc   >  1:2884178/1‑70 (MQ=255)
                                                                    |                                                         
CAGCCGGTACTGCGTCAGGTCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCGCCCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCG  >  minE/1827772‑1827897

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: ‑

GATK/CNVnator alignment

N/A