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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,792,242 C→T 38.0% T118I (ACC→ATC)  ubiA → p‑hydroxybenzoate octaprenyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,792,2420CT38.0% 71.6 / 83.9 79T118I (ACC→ATC) ubiAp‑hydroxybenzoate octaprenyltransferase
Reads supporting (aligned to +/- strand):  ref base C (32/17);  new base T (16/14);  total (48/31)
Fisher's exact test for biased strand distribution p-value = 3.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GCGCGCGCGCTGTTTGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGCGGTATACCCATCT  >  minE/2792175‑2792311
                                                                   |                                                                     
gcgcgcgcgcTGTTTGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCAt                                                                    <  1:1329881/71‑1 (MQ=255)
    gcgcgcTGTTTGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCtg                                                                >  1:2239041/1‑71 (MQ=255)
      gcgcTGTTTGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCAt                                                                    <  1:3193442/65‑1 (MQ=255)
        gcTGTTTGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCtgttgt                                                            <  1:1601927/71‑1 (MQ=255)
          tGTTTGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCtgttgt                                                            >  1:2511165/1‑69 (MQ=255)
          tGTTTGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTc                                                           >  1:2563368/1‑70 (MQ=255)
            tttGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCt                                                                 <  1:3890691/62‑1 (MQ=255)
            tttGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTCg                                                          <  1:84106/69‑1 (MQ=255)
            tttGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCg                                                          <  1:2918852/69‑1 (MQ=255)
             ttGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGAcc                                                                      <  1:3520629/56‑1 (MQ=255)
             ttGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCa                                                                     >  1:429520/1‑57 (MQ=255)
                        gTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTCGATTGCCGCGCTAgc                                            >  1:4074660/1‑71 (MQ=255)
                          aCTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTCGATTGCCGCGCTAgcgc                                          >  1:3708224/1‑71 (MQ=255)
                          aCTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAgcgc                                          >  1:546495/1‑71 (MQ=255)
                          aCTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAg                                             >  1:4039783/1‑68 (MQ=255)
                           cTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTCGa                                                         >  1:3918082/1‑55 (MQ=255)
                           cTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTc                                                                  >  1:3375641/1‑46 (MQ=255)
                           cTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAgcgc                                          <  1:865090/70‑1 (MQ=255)
                           cTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCt                                         >  1:2593891/1‑71 (MQ=255)
                           cTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCt                                         >  1:3395797/1‑71 (MQ=255)
                             gATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGa                                                         >  1:1045068/1‑53 (MQ=255)
                              acttCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGa                                                         >  1:2191128/3‑52 (MQ=255)
                              aTTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTc                                                                  >  1:3843228/1‑43 (MQ=255)
                              aTTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTCGATTGCCgcgc                                                >  1:158579/1‑61 (MQ=255)
                              aTTTCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTCGATTGCCgcgc                                                >  1:675237/1‑61 (MQ=255)
                              aTTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGa                                                         >  1:3169847/1‑52 (MQ=255)
                              aTTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCt                                         >  1:3550586/1‑68 (MQ=255)
                              aTTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTgg                                       <  1:4138066/70‑1 (MQ=255)
                              aTTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATCCTGTTGTCGATTGCCGCGCTAGCGCTgg                                       <  1:893493/70‑1 (MQ=255)
                               tttCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTc                                                           <  1:2977406/49‑1 (MQ=255)
                               tttCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTc                                                           <  1:3099614/49‑1 (MQ=255)
                               tttCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCg                                                          <  1:621737/50‑1 (MQ=255)
                                ttCGTTTTTACTGGTGCTGACGCTGAATACGATGATCAt                                                                    <  1:2817630/39‑1 (MQ=255)
                                ttCGTTTTTACTGGTGCTGACGCTGAATACGATGATCAt                                                                    <  1:3693721/39‑1 (MQ=255)
                                ttCGTTTTTACTGGTGCTGACCCTGAATACGATGACCATTCTGTTGTCGa                                                         >  1:3143047/1‑50 (MQ=255)
                                 tCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTCGa                                                         >  1:1170710/1‑49 (MQ=255)
                                 tCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTCGATTGcc                                                    >  1:1863092/1‑54 (MQ=255)
                                 tCGTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTCGATTGc                                                     <  1:2178955/53‑1 (MQ=255)
                                 tCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCtgt                                                               >  1:2636958/1‑43 (MQ=255)
                                 tCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCtgt                                                               >  1:3529102/1‑43 (MQ=255)
                                 tCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGAt                                                        >  1:1046245/1‑50 (MQ=255)
                                  cGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAg                                             <  1:1980400/60‑1 (MQ=255)
                                   gTTTTTACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTAGa                                                         >  1:275610/1‑47 (MQ=38)
                                    tttttACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGt                                    <  1:554663/67‑1 (MQ=255)
                                    tttttACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGt                                    <  1:554717/67‑1 (MQ=255)
                                      tttACTGGTGCTGACGCTGAATACGATGATCATTCtgtt                                                              >  1:422831/1‑39 (MQ=255)
                                      tttACTGGTGCTGACGCTGAATACGATGATCATTCTGTTGTCGATTGCCGCGCTAgc                                            <  1:1584852/57‑1 (MQ=255)
                                      tttACTGGTGCTGACGCTGAATACGATGACCATTCtgt                                                               >  1:354845/1‑38 (MQ=255)
                                             gTGCTGACGCTGAATACGATGATCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGtt                       >  1:2996428/1‑71 (MQ=255)
                                             gTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGtt                       >  1:1067605/1‑71 (MQ=255)
                                             gTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGtt                       >  1:722056/1‑71 (MQ=255)
                                             gTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGtt                       >  1:570782/1‑71 (MQ=255)
                                              tGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCg                                     <  1:479589/56‑1 (MQ=255)
                                              cgCTGGCGCTGAATACGATGACCATTCTGTTGTCGATTGcc                                                    >  1:2699063/2‑41 (MQ=255)
                                               gCTGACGCTGAATACGATGATCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTggg                                 >  1:1629527/1‑59 (MQ=255)
                                               gCTGACGCTGAATACGATGATCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTAc                            <  1:3959411/64‑1 (MQ=255)
                                               gCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGt                                    >  1:1192006/1‑56 (MQ=255)
                                               gCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGgtg                               >  1:1427386/1‑61 (MQ=255)
                                                cTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAgc                                            <  1:1696680/47‑1 (MQ=255)
                                                cTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGgt                                >  1:3125004/1‑59 (MQ=255)
                                                cTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTAt                    >  1:1765735/1‑71 (MQ=255)
                                                cTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTAt                    >  1:2912339/1‑71 (MQ=255)
                                                   aCGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGa                  <  1:1438867/70‑1 (MQ=255)
                                                     gCTGAATACGATGATCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGc               <  1:1802686/71‑1 (MQ=255)
                                                     gCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGc               >  1:2745277/1‑71 (MQ=255)
                                                        gAATACGATGATCATTCTGTTGTCGATTGCCGCGCTa                                              >  1:1576547/1‑37 (MQ=255)
                                                        gAATACGATGATCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGgtg                               >  1:3241632/1‑52 (MQ=255)
                                                         aaTACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGCgg             <  1:749084/69‑1 (MQ=255)
                                                         aaTACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGCGGta           >  1:2973190/1‑71 (MQ=255)
                                                          aTACGATGATCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGCGGta           >  1:2726191/1‑70 (MQ=255)
                                                          aTACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGCgg             <  1:2568756/68‑1 (MQ=255)
                                                           tACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTgg                                  >  1:3614047/1‑46 (MQ=255)
                                                           tACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTgg                                  >  1:1642171/1‑46 (MQ=255)
                                                             cGATGATCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGCgg             <  1:1276386/65‑1 (MQ=255)
                                                             cGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGAGTGGGTGTACCCGTTTATGAAGCGGTATAca       >  1:3995939/1‑70 (MQ=255)
                                                               aTGATCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGCGGTATACCCa     <  1:1567026/71‑1 (MQ=255)
                                                               aTGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTAccc                          >  1:328508/1‑50 (MQ=255)
                                                                  aCCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCg                         <  1:1298472/48‑1 (MQ=255)
                                                                  aCCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGCGGTATACCCATCt  <  1:1019839/71‑1 (MQ=255)
                                                                  aCCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGCGGTATACCCATCt  <  1:2290864/71‑1 (MQ=255)
                                                                   |                                                                     
GCGCGCGCGCTGTTTGTCGTGCTGGTACTGATTTCGTTTTTACTGGTGCTGACGCTGAATACGATGACCATTCTGTTGTCGATTGCCGCGCTAGCGCTGGCGTGGGTGTACCCGTTTATGAAGCGGTATACCCATCT  >  minE/2792175‑2792311

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