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 2,666,200 C→T 43.0% Q604Q (CAG→CAA)  malT ← DNA‑binding transcriptional activator, maltotriose‑ATP‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,666,2000CT43.0% 25.7 / 57.6 79Q604Q (CAG→CAA) malTDNA‑binding transcriptional activator, maltotriose‑ATP‑binding
Reads supporting (aligned to +/- strand):  ref base C (28/17);  new base T (17/17);  total (45/34)
Fisher's exact test for biased strand distribution p-value = 3.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.97e-01

GCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCTTCGGCTTCATCCAGCCGCGCCCAGG  >  minE/2666150‑2666267
                                                  |                                                                   
gCCAGCGAGCATTGAATCAACATTGCCAGGTACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:2386031/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:2695990/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:50477/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:3213876/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:1523344/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:1904731/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:1474212/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:3161253/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:3078077/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:2092193/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:1359047/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:2513222/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:1284509/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:1218162/69‑1 (MQ=255)
gCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:2759956/69‑1 (MQ=255)
 ccAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:296750/68‑1 (MQ=255)
  cAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTc                                                 <  1:987047/69‑1 (MQ=255)
  cAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTc                                                 <  1:1667061/69‑1 (MQ=255)
  cAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTc                                                 <  1:650762/69‑1 (MQ=255)
             gAATCAACATTGGCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTc                                                 <  1:1467406/58‑1 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTc                                                 <  1:459030/58‑1 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTc                                                 <  1:136463/58‑1 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTc                                                 <  1:829870/58‑1 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTc                                                 <  1:1525736/58‑1 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTc                                                 <  1:1820341/58‑1 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTa                                       >  1:1856779/1‑68 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTAc                                      >  1:2871727/1‑69 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTAc                                      >  1:2432659/1‑69 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTAc                                      >  1:2945473/1‑69 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTAc                                      >  1:3157174/1‑69 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTAc                                      >  1:578343/1‑69 (MQ=255)
             gAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTAc                                      >  1:3321799/1‑69 (MQ=255)
             gAATCAACATTGACAGTCACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACt                                                   <  1:1411680/56‑1 (MQ=255)
              aaTGAACATTGCGAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAATACTTc                                                 <  1:2146522/57‑1 (MQ=255)
              aaTCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTc                                                 <  1:437264/57‑1 (MQ=255)
                tCAACATTGCCAGGCACTGAAGCTGTTGCTGTGTCTGATAAGACGACAAGACTTCAATCCCGCTAcgcg                                   <  1:890331/69‑1 (MQ=255)
                tCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTAcgcg                                   <  1:3169235/69‑1 (MQ=255)
                tCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTAcgcg                                   <  1:385516/69‑1 (MQ=255)
                 cAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTAcgcg                                   <  1:1910860/68‑1 (MQ=255)
                  aaCATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCa                                                >  1:1818356/1‑54 (MQ=255)
                  aaCATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGcc                                 >  1:2390655/1‑69 (MQ=255)
                  aaCATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGcc                                 >  1:2905173/1‑69 (MQ=255)
                  aaCATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGcc                                 >  1:79398/1‑69 (MQ=255)
                  aaCATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGcc                                 >  1:338429/1‑69 (MQ=255)
                  aaCATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGcc                                 >  1:495737/1‑69 (MQ=255)
                  aaCATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGcc                                 >  1:2610825/1‑69 (MQ=255)
                  aaCATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGcc                                 >  1:259683/1‑69 (MQ=255)
                  aaCATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGcc                                 >  1:1321096/1‑69 (MQ=255)
                  aaCATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGcc                                 >  1:1587902/1‑69 (MQ=255)
                  aaCATAGCCAGGCACTGAAGCTGTTGCTGTGGCTGAAAAGACGACAAGACTTc                                                 >  1:2040625/1‑53 (MQ=255)
                        gCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCGCGCTACGCGCCGACGCt                           >  1:2940912/1‑69 (MQ=255)
                        gCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCt                           >  1:57468/1‑69 (MQ=255)
                        gCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCt                           >  1:1553251/1‑69 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGAc                                                    >  1:1432760/1‑38 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCt                           >  1:2023820/1‑63 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:1080210/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:1551799/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:2379745/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:2689766/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:1716894/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:437052/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:1761202/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:2380735/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:3322206/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:602542/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:3179513/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:1463283/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:316795/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:2039165/1‑68 (MQ=255)
                              cACTGAAGCTGTTGCTGTGGTTGATAAGACGACAAGACTTCAATCCCGCTGCGCGCCGACGCTTCGGc                      >  1:769342/1‑68 (MQ=255)
                                  gAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCaa                                               >  1:2974468/1‑39 (MQ=255)
                                  gAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCTTCGGCTTCa                  >  1:2980733/1‑68 (MQ=255)
                                              gtgGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCTTCGGCTTCATCCAGCCGCGcc      <  1:1046053/68‑1 (MQ=255)
                                              gtgGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCTTCGGCTTCATCCAGCCGCGcc      <  1:1833914/68‑1 (MQ=255)
                                                 tcTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCTTCGGCTTCATCCAGCCGCGCCCAgg  >  1:1769482/2‑69 (MQ=255)
                                                 gCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCTGACGCTTCGGCTTCATCCAGCCGCGCCCAgg  >  1:1768852/1‑69 (MQ=255)
                                                 gCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCTTCGGCTTCATCCAGCCGCGCCCAgg  >  1:1073024/1‑69 (MQ=255)
                                                 gCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCTTCGGCTTCATCCAGCCGCGCCCAgg  >  1:152224/1‑69 (MQ=255)
                                                 gCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCTTCGGCTTCATCCAGCCGCGCCCAgg  >  1:1768880/1‑69 (MQ=255)
                                                 gCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCTTCGGCTTCATCCAGCCGCGCCCAgg  >  1:2345833/1‑69 (MQ=255)
                                                  |                                                                   
GCCAGCGAGCATTGAATCAACATTGCCAGGCACTGAAGCTGTTGCTGTGGCTGATAAGACGACAAGACTTCAATCCCGCTACGCGCCGACGCTTCGGCTTCATCCAGCCGCGCCCAGG  >  minE/2666150‑2666267

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: ‑

GATK/CNVnator alignment

N/A