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 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,599,135 A→T 29.5% I33I (ATT→ATA)  gor ← glutathione oxidoreductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,599,1350AT29.5% 86.2 / 51.0 61I33I (ATT→ATA) gorglutathione oxidoreductase
Reads supporting (aligned to +/- strand):  ref base A (25/18);  new base T (15/3);  total (40/21)
Fisher's exact test for biased strand distribution p-value = 7.90e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-01

CACATCACTTTTTTCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGATACCGCCGCTGCCGCCGCCG  >  minE/2599073‑2599204
                                                              |                                                                     
cacaTCACTTTTTTCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAgcgc                                                               <  1:611674/71‑1 (MQ=255)
      aCTTTTTTCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCTATCAgc                                                                 >  1:502609/1‑63 (MQ=255)
      aCTTTTTTCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCTATCAgc                                                                 >  1:2503417/1‑63 (MQ=255)
      aCTTTTTTCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCTATCAGCGCACAttt                                                         <  1:1649027/71‑1 (MQ=255)
      aCTTTTTTCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAg                                                                  >  1:2779727/1‑62 (MQ=255)
      aCTTTTTTCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACAttt                                                         >  1:3801954/1‑71 (MQ=255)
      aCTTTTTTCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACAttt                                                         >  1:2001269/1‑71 (MQ=255)
      aCTTTTTTCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACAttt                                                         >  1:1473435/1‑71 (MQ=255)
          ttttCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCTATCAGCGCACATTTCTgg                                                     >  1:2176152/1‑71 (MQ=255)
          ttttCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACAttt                                                         >  1:1880418/1‑67 (MQ=255)
          ttttCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTg                                                      >  1:1238572/1‑70 (MQ=255)
          ttttCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTg                                                      >  1:1692615/1‑70 (MQ=255)
          ttttCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTg                                                      >  1:315405/1‑70 (MQ=255)
          ttttCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTg                                                      >  1:2723358/1‑70 (MQ=255)
               ggCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCTATCAGCGCACATTTCTGGCCGTa                                                <  1:513276/71‑1 (MQ=255)
                     caGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATc                                                                    >  1:776518/1‑45 (MQ=255)
                     caGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATc                                                                    >  1:2625968/1‑45 (MQ=255)
                       gCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCa                                                                   <  1:2098059/44‑1 (MQ=255)
                         cAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGTGca                                                              <  1:2445678/47‑1 (MQ=255)
                         cAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGca                                                              <  1:2017411/47‑1 (MQ=255)
                         cAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGca                                                              <  1:2032834/47‑1 (MQ=255)
                          aaCATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACAt                                                           <  1:930479/49‑1 (MQ=255)
                          aaCATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACAt                                                           <  1:2084175/49‑1 (MQ=255)
                            cATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCgg                                   >  1:1813482/1‑71 (MQ=255)
                            cATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCgg                                   >  1:3920496/1‑71 (MQ=255)
                              tttACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGt                                  <  1:1209065/70‑1 (MQ=255)
                                tACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATa                                            >  1:2384874/1‑58 (MQ=255)
                                tACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATa                                            >  1:1418861/1‑58 (MQ=255)
                                 aCGCAGGTGCCGCCCAGCTCTTTGGCTTCTATCAGCGcac                                                             >  1:3864265/1‑40 (MQ=255)
                                 aCGCAGGTGCCGCCCAGCTCTTTGGCTTCTATCAGCGCACATTTCt                                                       >  1:535477/1‑46 (MQ=255)
                                 aCGCAGGTGCCGCCCAGCTCTTTGGCTTCTATCAGCGCACATTTCt                                                       >  1:2432582/1‑46 (MQ=255)
                                 aCGCAGGTGCCGCCCAGCTCTTTGGCTTCTATCAGCGCACATTTCt                                                       >  1:2415091/1‑46 (MQ=255)
                                 aCGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGa                               <  1:1403488/70‑1 (MQ=255)
                                 aCGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGa                               <  1:272070/70‑1 (MQ=255)
                                 aCGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGa                               <  1:3692887/70‑1 (MQ=255)
                                 aCGCAGGTGC‑‑CCCAGCTCTTTGGCTTCTATCAGCGCACATTTCt                                                       >  1:1465357/1‑44 (MQ=255)
                                  cGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGa                               <  1:193015/69‑1 (MQ=255)
                                  cGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATg                             <  1:4156975/71‑1 (MQ=255)
                                         gccgccCAGCTCTTTGGCTTCTATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGa                      >  1:3222497/1‑71 (MQ=255)
                                         gccgccCAGCTCTTTGGCTTCTATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGa                      >  1:1515498/1‑71 (MQ=255)
                                         gccgccCAGCTCTTTGGCTTCTATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGa                      >  1:3227311/1‑71 (MQ=255)
                                         gccgccCAGCTCTTTGGCTTCTATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGa                      >  1:2614285/1‑71 (MQ=255)
                                          ccgccCAGCTCTTTGGCTTCTATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGa                      >  1:3602067/1‑70 (MQ=255)
                                            gccCAGCTCTTTGGCTTCTATCAGCGCACATTTCTGGCCg                                                  <  1:1728196/40‑1 (MQ=255)
                                                  ctctTTGGCTTCTATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGATACcgccgc             >  1:2569807/1‑71 (MQ=255)
                                                   tctTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGc                        <  1:1226816/59‑1 (MQ=255)
                                                    ctTTGGCTTCAATCAGCGCACATTTCTGGCCGTACa                                              >  1:1045735/1‑36 (MQ=255)
                                                    ctTTGGCTTCAATCAGCGCACATTTCTGGCCGTACa                                              >  1:2326506/1‑36 (MQ=255)
                                                    ctTTGGCTTCAATCAGCGCACATTTCTGGCCGTACa                                              >  1:2564742/1‑36 (MQ=255)
                                                    ctTTGGCTTCAATCAGCGCACATTTCTGGCCGTACa                                              >  1:4097198/1‑36 (MQ=255)
                                                    ctTTGGCTTCAATCAGCGCACATTTCTGGCCGTACa                                              >  1:2779521/1‑36 (MQ=255)
                                                    ctTTGGCTTCAATCAGCGCACATTTCTGGCCGTACa                                              >  1:750859/1‑36 (MQ=255)
                                                    ctTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGa                               >  1:1451089/1‑51 (MQ=255)
                                                     tttGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGtt                                 <  1:2076934/48‑1 (MQ=255)
                                                     tttGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGtt                                 <  1:3467911/48‑1 (MQ=255)
                                                     tttGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGtt                                 <  1:4165686/48‑1 (MQ=255)
                                                     tttGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGtt                                 <  1:1901346/48‑1 (MQ=255)
                                                      ttGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGt                                  >  1:3431651/1‑46 (MQ=255)
                                                      ttGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGt                                  >  1:2426677/1‑46 (MQ=255)
                                                       tGGCTTCTATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGATACCGCCGCTgccg        >  1:68136/1‑71 (MQ=255)
                                                       tGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGATACCGCCGCTgcc         >  1:2616020/1‑70 (MQ=255)
                                                              aaTCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGATACCGCCGCTGccgccgccg  <  1:417444/70‑1 (MQ=255)
                                                              aaTCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGATACCGCCGCTGccgccgccg  <  1:2924650/70‑1 (MQ=255)
                                                              |                                                                     
CACATCACTTTTTTCGGCACACAGCCAACATTTACGCAGGTGCCGCCCAGCTCTTTGGCTTCAATCAGCGCACATTTCTGGCCGTACATAGCCGCGCGGTTGATGGAGGCGATACCGCCGCTGCCGCCGCCG  >  minE/2599073‑2599204

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