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 2,575,573 T→C 44.3% Y416Y (TAT→TAC)  glyS → glycine tRNA synthetase, beta subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,575,5730TC44.3% 11.9 / 55.0 70Y416Y (TAT→TAC) glySglycine tRNA synthetase, beta subunit
Reads supporting (aligned to +/- strand):  ref base T (7/32);  new base C (22/9);  total (29/41)
Fisher's exact test for biased strand distribution p-value = 9.28e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

CTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGTTTTGC  >  minE/2575514‑2575641
                                                           |                                                                    
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCATGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:196115/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATTCACTATGCGCGTCAc                                                             <  1:3267420/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGTACTATGCGCGTCAc                                                             <  1:1731946/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCTCGTCAc                                                             <  1:3083/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:103780/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:202066/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:2228262/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:2403431/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:2406089/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:1707525/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:2711041/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:2882493/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:2893535/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:3342994/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:1353478/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:1344410/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:1336429/69‑1 (MQ=255)
cTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:464064/69‑1 (MQ=255)
      aCCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGc                                                       <  1:1532579/69‑1 (MQ=255)
      aCCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGc                                                       <  1:1130288/69‑1 (MQ=255)
        cAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCAc                                                             <  1:1089406/61‑1 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:2310499/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:3299688/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:800138/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:2043488/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:770356/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:672057/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:558578/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:2536970/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:3217864/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:1842094/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:1045940/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:1088346/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:1189075/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:1428827/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:1477424/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:1496446/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:1524453/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGaa                                                    >  1:1664028/1‑69 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGa                                                     >  1:3374707/1‑68 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGa                                                     >  1:1026791/1‑68 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGa                                                     >  1:460526/1‑68 (MQ=255)
         aaCATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGAAGCACTACGCGCGTCACGATGGCGaa                                                    >  1:2689726/1‑69 (MQ=255)
            aTGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGAAGCg                                                 <  1:3410225/69‑1 (MQ=255)
            aTGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGAAGCg                                                 <  1:2469232/69‑1 (MQ=255)
            aTGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGAAGCg                                                 <  1:168941/69‑1 (MQ=255)
            aTGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGAAGCg                                                 <  1:3372552/69‑1 (MQ=255)
            aTGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGAAGCg                                                 <  1:39702/69‑1 (MQ=255)
            aTGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGAAGCg                                                 <  1:1633855/69‑1 (MQ=255)
            aTGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGAAGCg                                                 <  1:405282/69‑1 (MQ=255)
            aTGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGAAGCg                                                 <  1:1222322/69‑1 (MQ=255)
            aTGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTACGCGCGTCACGATGGCGAAGCg                                                 <  1:431949/69‑1 (MQ=255)
                          cACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGt                                   >  1:1742239/1‑69 (MQ=255)
                                 acCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:2178010/69‑1 (MQ=255)
                                 acCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:1137730/69‑1 (MQ=255)
                                 acCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:792724/69‑1 (MQ=255)
                                 acCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:197542/69‑1 (MQ=255)
                                 acCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:1719163/69‑1 (MQ=255)
                                 acCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:346129/69‑1 (MQ=255)
                                 acCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:3431798/69‑1 (MQ=255)
                                 acCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:2215826/69‑1 (MQ=255)
                                 acCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:3055787/69‑1 (MQ=255)
                                  cccAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:2247097/68‑1 (MQ=255)
                                  cccAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTg                            <  1:570621/68‑1 (MQ=255)
                                                      cACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGt       >  1:1765270/1‑69 (MQ=255)
                                                      cACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGt       >  1:2849559/1‑69 (MQ=255)
                                                      cACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGt       >  1:1817946/1‑69 (MQ=255)
                                                      cACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGt       >  1:2365051/1‑69 (MQ=255)
                                                      cACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGt       >  1:899928/1‑69 (MQ=255)
                                                      cACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGt       >  1:900046/1‑69 (MQ=255)
                                                           tGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGTTTTGc  >  1:1415508/1‑69 (MQ=255)
                                                           tGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGTTTTGc  >  1:413410/1‑69 (MQ=255)
                                                           tGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGTTTTGc  >  1:1587376/1‑69 (MQ=255)
                                                           tGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGTTTTGc  >  1:2691978/1‑69 (MQ=255)
                                                           |                                                                    
CTGATGACCAACATGGTCTTCGAGTTCACCGACACCCAGGGCGTTATGGGGATGCACTATGCGCGTCACGATGGCGAAGCGGAAGATGTCGCGGTGGCGCTGAATGAGCAGTATCAGCCGCGTTTTGC  >  minE/2575514‑2575641

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