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 2,557,493 C→T 48.5% S49S (TCC→TCT)  secB → protein export chaperone

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,557,4930CT48.5% 4.5 / 87.1 99S49S (TCC→TCT) secBprotein export chaperone
Reads supporting (aligned to +/- strand):  ref base C (24/27);  new base T (36/12);  total (60/39)
Fisher's exact test for biased strand distribution p-value = 7.14e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.45e-01

Only 100 of 107 total aligned reads displayed.

GCCGCACGTTTTCCAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGTAACGGCCTCTTTGGGCGAAGA  >  minE/2557430‑2557558
                                                               |                                                                 
gccgcACGTTTTCCAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACt                                                              >  1:755717/1‑69 (MQ=255)
gccgcACGTTTTCCAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACt                                                              >  1:533001/1‑69 (MQ=255)
gccgcACGTTTTCCAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACt                                                              >  1:1367269/1‑69 (MQ=255)
 ccgcACGTTTTCCAGAAAGATTGGCAGCCAGAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTg                                                             <  1:918617/69‑1 (MQ=255)
 ccgcACGTTTTCCAGAAAGATTGGCAGCCAGAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTg                                                             <  1:285362/69‑1 (MQ=255)
 ccgcACGTTTTCCAGAAAGATTGGCAGCCAGAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTg                                                             <  1:3417040/69‑1 (MQ=255)
 ccgcACGTTTTCCAGAAAGATTGGCAGCCAGAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTg                                                             <  1:2614754/69‑1 (MQ=255)
 ccgcACGTTTTCCAGAAAGATTGGCAGCCAGAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTg                                                             <  1:1059663/69‑1 (MQ=255)
 ccgcACGTTTTCCAGAAAGATTGGCAGCCAGAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTg                                                             <  1:1810657/69‑1 (MQ=255)
 ccgcACGTTTTCCAGAAAGATTGGCAGCCAGAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTg                                                             <  1:3091100/69‑1 (MQ=255)
  cgcACGTTTTCCAGAAAGATTGGCAGCCAGAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTg                                                             <  1:897485/68‑1 (MQ=255)
       gTTTTCCAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGAt                                                       <  1:3194472/69‑1 (MQ=255)
       gTTTTCCAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGAt                                                       <  1:608730/69‑1 (MQ=255)
        ttttCCAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAg                                                         >  1:854400/1‑66 (MQ=255)
          ttCCAGAAAGATTGGCAACCAGAAGTTAAACTT‑ATCTGGATACGGCATCTTCCCAACTGGCAGATGACg                                                   <  1:1304849/69‑1 (MQ=255)
            ccAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACg                                                   <  1:2124297/68‑1 (MQ=255)
            ccAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACg                                                   <  1:2773138/68‑1 (MQ=255)
            ccAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACg                                                   <  1:484707/68‑1 (MQ=255)
                 aaGATTGGCAGCCAGAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTg                                                             <  1:651320/53‑1 (MQ=255)
                 aaGATTGGCAACCAGATGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACg                                             <  1:3299507/69‑1 (MQ=255)
                 aaGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGtata                                               >  1:1958576/1‑67 (MQ=255)
                 aaGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGtata                                               >  1:787315/1‑67 (MQ=255)
                 aaGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGtata                                               >  1:251593/1‑67 (MQ=255)
                 aaGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGtata                                               >  1:289510/1‑67 (MQ=255)
                 aaGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACg                                             <  1:945559/69‑1 (MQ=255)
                 aaGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACg                                             <  1:1735681/69‑1 (MQ=255)
                 aaGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACg                                             <  1:3340351/69‑1 (MQ=255)
                 aaGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACg                                             <  1:569422/69‑1 (MQ=255)
                 aaGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACg                                             <  1:1318925/69‑1 (MQ=255)
                 aaGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACg                                             <  1:808803/69‑1 (MQ=255)
                      tGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTccc                                                                  >  1:453484/1‑43 (MQ=255)
                      tGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTccc                                                                  >  1:633144/1‑43 (MQ=255)
                      tGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTccc                                                                  >  1:1057564/1‑43 (MQ=255)
                      tGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTccc                                                                  >  1:2120141/1‑43 (MQ=255)
                      tGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTccc                                                                  >  1:1737390/1‑43 (MQ=255)
                      tGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTccc                                                                  >  1:2005616/1‑43 (MQ=255)
                      tGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTccc                                                                  >  1:1464654/1‑43 (MQ=255)
                      tGGCAACCAGAAGTTAAACTAGATCTGGATACGGCATCTTccc                                                                  >  1:386209/1‑43 (MQ=255)
                       ggCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTgg                                       <  1:615000/69‑1 (MQ=255)
                       ggCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTgg                                       <  1:747554/69‑1 (MQ=255)
                       ggCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTgg                                       <  1:2769231/69‑1 (MQ=255)
                       ggCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTgg                                       <  1:3083455/69‑1 (MQ=255)
                       ggCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTgg                                       <  1:61309/69‑1 (MQ=255)
                       ggCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTgg                                       <  1:1148702/69‑1 (MQ=255)
                       ggCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTgg                                       <  1:1138347/69‑1 (MQ=255)
                        gCAACCAGAAGTTAAACTTGATCTGGAAACGGCATCTTCCCAACTGGCAGATGACg                                                   <  1:262579/56‑1 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:518288/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:1571322/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:3245988/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:1654053/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:3105609/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:1412289/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:661516/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:1484873/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:1441567/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:2368185/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:2056536/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:2675830/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:777520/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:2391944/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:1225753/1‑69 (MQ=255)
                               gAAGTTAAACTTGATCTGGATACGGCATCTTCTCAACTGGCAGATGACGTTTACGAAGTGGTACTGCgt                               >  1:2330649/1‑69 (MQ=255)
                                    tAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTAc                          >  1:2904102/1‑69 (MQ=255)
                                    tAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTAc                          >  1:1782289/1‑69 (MQ=255)
                                    tAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTAc                          >  1:2493179/1‑69 (MQ=255)
                                    tAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTAc                          >  1:1959659/1‑69 (MQ=255)
                                        cTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGt                       <  1:1701913/68‑1 (MQ=255)
                                        cTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGt                       <  1:343279/68‑1 (MQ=255)
                                        cTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGt                       <  1:1871393/68‑1 (MQ=255)
                                        cTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTAATGCGTGTTACCGt                       <  1:1285035/68‑1 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCATATGACGt                                                  >  1:2537039/1‑38 (MQ=37)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:1006797/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:1138782/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:544313/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:1290382/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:126208/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:736128/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:49965/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:2343878/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:1502903/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:3408795/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:1510273/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:2402333/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:3330729/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:2638201/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:3041234/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:2926288/1‑38 (MQ=255)
                                           gATCTGGATACGGCATCTTCTCAACTGGCAGATGACGt                                                  >  1:2866479/1‑38 (MQ=255)
                                             tCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGTAACGGc                 >  1:1972160/1‑69 (MQ=255)
                                             tCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGTAACGGc                 >  1:887350/1‑69 (MQ=255)
                                             tCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGTAACGGc                 >  1:2748878/1‑69 (MQ=255)
                                             tCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGTAACGGc                 >  1:556293/1‑69 (MQ=255)
                                                            ttCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGt                       >  1:167854/1‑48 (MQ=255)
                                                            ttCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGt                       >  1:257018/1‑48 (MQ=255)
                                                            ttCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGt                       >  1:842172/1‑48 (MQ=255)
                                                            ttCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGt                       >  1:1138911/1‑48 (MQ=255)
                                                            ttCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGTAACGGCCTCTTTGGGCgaaga  >  1:618458/1‑69 (MQ=255)
                                                            ttCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGTAACGGCCTCTTTGGGCgaaga  >  1:1328948/1‑69 (MQ=255)
                                                            ttCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGTAACGGCCTCTTTGGGCgaaga  >  1:1967515/1‑69 (MQ=255)
                                                            ttCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGTAACGGCCTCTTTGGGCgaaga  >  1:450955/1‑69 (MQ=255)
                                                               |                                                                 
GCCGCACGTTTTCCAGAAAGATTGGCAACCAGAAGTTAAACTTGATCTGGATACGGCATCTTCCCAACTGGCAGATGACGTATACGAAGTGGTACTGCGTGTTACCGTAACGGCCTCTTTGGGCGAAGA  >  minE/2557430‑2557558

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