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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,022,353 T→A 50.5% G470G (GGA→GGT)  uidA ← beta‑D‑glucuronidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,022,3530TA50.5% ‑2.4 / 123.3 99G470G (GGA→GGT) uidAbeta‑D‑glucuronidase
Reads supporting (aligned to +/- strand):  ref base T (24/25);  new base A (20/30);  total (44/55)
Fisher's exact test for biased strand distribution p-value = 4.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 103 total aligned reads displayed.

TTTTCCAGTACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGTCGCAGAA  >  minE/1022303‑1022421
                                                  |                                                                    
ttttCCAGAACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAg                                                     <  1:33598/68‑1 (MQ=255)
ttttCCAGAACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAg                                                     <  1:981517/68‑1 (MQ=255)
ttttCCAGAACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAg                                                     <  1:2029508/68‑1 (MQ=255)
ttttCCAGAACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAg                                                     <  1:1180365/68‑1 (MQ=255)
ttttCCAGAACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAg                                                     <  1:2469225/68‑1 (MQ=255)
ttttCCAGAACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAg                                                     <  1:2104427/68‑1 (MQ=255)
ttttCCAGAACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAg                                                     <  1:2708491/68‑1 (MQ=255)
ttttCCAGAACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAg                                                     <  1:657769/68‑1 (MQ=255)
ttttCCAGAACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAg                                                     <  1:2834832/68‑1 (MQ=255)
ttttCCAGAACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGCACATACCAACCGTAATAACGGTTCAg                                                     <  1:922442/68‑1 (MQ=255)
          ccTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGtaat                                                               >  1:3008671/1‑48 (MQ=255)
          ccTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGtaat                                                               >  1:2735033/1‑48 (MQ=255)
          ccTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGtaat                                                               >  1:470352/1‑48 (MQ=255)
          ccTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGgcacagcaca                                           >  1:31592/1‑68 (MQ=255)
          ccTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGgcacagcaca                                           >  1:2861016/1‑68 (MQ=255)
            ttCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACAt                                          >  1:1701631/1‑67 (MQ=255)
            ttCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACAt                                          >  1:2365740/1‑67 (MQ=255)
            ttCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACAt                                          >  1:2608646/1‑67 (MQ=255)
            ttCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACAt                                          >  1:2662385/1‑67 (MQ=255)
            ttCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACAt                                          >  1:1028998/1‑67 (MQ=255)
            ttCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGAACAGCACAt                                          >  1:3176623/1‑67 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAaga                                    <  1:1376682/66‑1 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAaga                                    <  1:1129218/66‑1 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGgcacag                                               >  1:1108965/1‑55 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAgaga                                  >  1:3013017/1‑68 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:2834743/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:2920793/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:2993294/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:1865455/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:3138041/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:2674012/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:1665824/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:1067761/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:1182665/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:1256683/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:139083/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:3380257/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:1492618/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:1539701/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:1574338/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGAt                                 >  1:169837/1‑69 (MQ=255)
                   ccGTTTCCAAATCGCCGCTTTGGACATACCAACCGTAATAACGGTTAAGGCACAGCACATCAAAGAGAt                                 >  1:3249293/1‑69 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCTCAGCACATCAAAGAGATCGCt                             <  1:565609/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCAGAGCACATCAAAGAGATCGCt                             <  1:1468408/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGATATCGCt                             <  1:439259/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:3374951/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:3087129/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:683290/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:733506/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:3193470/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:967478/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:982757/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:1498148/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:2150127/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:2144059/69‑1 (MQ=255)
                       ttCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCt                             <  1:1815305/69‑1 (MQ=255)
                        tCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCAAATCAAAGAGATCGCt                             <  1:3299196/68‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCTCATCAAAGAGATCGCTGATGGTAt                     <  1:186638/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:1323615/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:1395768/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:382719/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:1560849/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:325351/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:1616483/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:3140954/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:3128917/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:937715/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:3041210/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:2721740/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:2767870/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:1079636/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:2053177/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:1912351/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:1886190/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:3018749/69‑1 (MQ=255)
                               cgccgcTTTGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATAAAAGAGATCGCTGATGGTAt                     <  1:819421/69‑1 (MQ=255)
                                   gcTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGgt                 <  1:70640/69‑1 (MQ=255)
                                   gcTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGgt                 <  1:1328054/69‑1 (MQ=255)
                                     tttGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGACATCGCt                             <  1:283/55‑1 (MQ=255)
                                      ttGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGtgtg              <  1:1172128/69‑1 (MQ=255)
                                      ttGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGtgtg              <  1:2327273/69‑1 (MQ=255)
                                      ttGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGtgtg              <  1:1410673/69‑1 (MQ=255)
                                      ttGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGtgtg              <  1:1150001/69‑1 (MQ=255)
                                       tGGACATACCAACCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTAt                     <  1:2157524/61‑1 (MQ=255)
                                              aCCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGt         >  1:766545/1‑66 (MQ=255)
                                              aCCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGt         >  1:1209401/1‑66 (MQ=255)
                                              aCCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGt         >  1:727471/1‑66 (MQ=255)
                                              aCCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGt         >  1:105589/1‑66 (MQ=255)
                                              aCCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGt         >  1:675477/1‑66 (MQ=255)
                                              aCCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGt         >  1:1654162/1‑66 (MQ=255)
                                              aCCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGt         >  1:1683159/1‑66 (MQ=255)
                                              aCCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGt         >  1:1707462/1‑66 (MQ=255)
                                              aCCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGt         >  1:314659/1‑66 (MQ=255)
                                              aCCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGt         >  1:3114949/1‑66 (MQ=255)
                                               ccATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGTCGc      >  1:2060286/1‑68 (MQ=255)
                                               ccATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGTCGc      >  1:2857566/1‑68 (MQ=255)
                                                  tCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGTCGCAGaa  <  1:1210565/69‑1 (MQ=255)
                                                  tCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGTCGCAGaa  <  1:1330188/69‑1 (MQ=255)
                                                  tCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGTCGCAGaa  <  1:3209983/69‑1 (MQ=255)
                                                  tCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGTCGCAGaa  <  1:186478/69‑1 (MQ=255)
                                                  |                                                                    
TTTTCCAGTACCTTCTCTGCCGTTTCCAAATCGCCGCTTTGGACATACCATCCGTAATAACGGTTCAGGCACAGCACATCAAAGAGATCGCTGATGGTATCGGTGTGAGCGTCGCAGAA  >  minE/1022303‑1022421

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A