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 775,331 C→T 65.8% G318G (GGC→GGT)  icd → isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE775,3310CT65.8% 20.1 / 16.5 35G318G (GGC→GGT) icdisocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand):  ref base C (7/5);  new base T (7/16);  total (14/21)
Fisher's exact test for biased strand distribution p-value = 1.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

ATGTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGCGGTATCGGTATCGCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCA  >  minE/775267‑775389
                                                                |                                                          
atgTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggta                                                        >  1:922987/1‑69 (MQ=255)
atgTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggta                                                        >  1:512675/1‑69 (MQ=255)
atgTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggta                                                        >  1:491113/1‑69 (MQ=255)
atgTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggta                                                        >  1:3112337/1‑69 (MQ=255)
atgTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggta                                                        >  1:1560415/1‑69 (MQ=255)
atgTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggta                                                        >  1:1945837/1‑69 (MQ=255)
atgTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggt                                                         >  1:3389648/1‑68 (MQ=255)
   ttATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatc                                                      >  1:113651/1‑68 (MQ=255)
   ttATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatc                                                      >  1:3392192/1‑68 (MQ=255)
   ttATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatc                                                      >  1:3095510/1‑68 (MQ=255)
   ttATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatc                                                      >  1:2931121/1‑68 (MQ=255)
   ttATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatc                                                      >  1:1975961/1‑68 (MQ=255)
   ttATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatc                                                      >  1:1974388/1‑68 (MQ=255)
     aTCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:3170704/69‑1 (MQ=255)
     aTCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:2997003/69‑1 (MQ=255)
     aTCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:3016185/69‑1 (MQ=255)
     aTCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:2005675/69‑1 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatctgt                                                   <  1:1832796/66‑1 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggtat                                                 >  1:323012/1‑68 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:1464220/66‑1 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:1450391/66‑1 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:2303270/66‑1 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:2176850/66‑1 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:2111568/66‑1 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:63891/66‑1 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:1514256/66‑1 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:2883178/66‑1 (MQ=255)
        gCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGCggtatcggtatc                                                >  1:3110521/1‑69 (MQ=255)
        gCCTGAATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGCggtatcggtatc                                                >  1:2487442/1‑69 (MQ=255)
         ccTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   <  1:554822/65‑1 (MQ=255)
            gTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGCGGTATCGGTATCGccc                                            >  1:330416/1‑69 (MQ=255)
               tGAACCTGAACGGTGACTACATTTGTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   >  1:2695925/1‑59 (MQ=255)
               tGAACCTGAACGGTGACTACATTTCTGCCGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   >  1:1356292/1‑59 (MQ=255)
               tGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   >  1:2273255/1‑59 (MQ=255)
               tGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   >  1:3365540/1‑59 (MQ=255)
               tGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   >  1:1347738/1‑59 (MQ=255)
               tGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   >  1:343546/1‑59 (MQ=255)
               tGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   >  1:1893326/1‑59 (MQ=255)
               tGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGCTTGGcggtatcggt                                                   >  1:1017251/1‑59 (MQ=255)
               tGAACCTGAACGGTGACTACAATTCTGACGCCCTGGCAGCGCAGGTTGGcggtatcggt                                                   >  1:2769184/1‑59 (MQ=255)
                    cTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGCGGTATCGGTATCGCCCCTGGTGCa                                    <  1:1715096/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGTTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:3030795/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:1529713/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:2665349/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:2618193/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:2555419/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:2540510/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:2486650/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:3134522/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:2176113/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:2471326/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:882427/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:652842/69‑1 (MQ=255)
                         cGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:1637771/69‑1 (MQ=255)
                          ggTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:525659/68‑1 (MQ=255)
                          ggTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:2064830/68‑1 (MQ=255)
                          ggTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACAt                               <  1:2529456/68‑1 (MQ=255)
                                 aCATTTCTGACGCCCTGGCAGCGCAGGTTGGCGGTATCGGTATCGCCCCTGGTGCAAACATCGGTGACg                       <  1:530581/69‑1 (MQ=255)
                                 aCATTTCTGACGCCCTGGCAGCGCAGGTTGGCGGTATCGGTATCGCCCCTGGTGCAAACATCGGTGACg                       <  1:3161336/69‑1 (MQ=255)
                                 aCATTTCTGACGCCCTGGCAGCGCAGGTTGGCGGTATCGGTATCGCCCCTGGTGCAAACATCGGTGACg                       <  1:288716/69‑1 (MQ=255)
                                 aCATTTCTGACGCCCTGGCAGCGCAGGTTGGCGGTATCGGTATCGCCCCTGGTGCAAACATCGGTGACg                       <  1:1598977/69‑1 (MQ=255)
                                    tttCTGACGCCCTGGCAGCGCAGGTTGGCGGTATCGGTATCGCCCCTGGTGCAAACATCGGTGACGAAt                    >  1:3390580/1‑69 (MQ=255)
                                             cccTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACATCGGTGACGAATgcgc                >  1:1677111/1‑64 (MQ=255)
                                             cccTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACATCGGTGACGAATGCGCCCTg            >  1:2299313/1‑68 (MQ=255)
                                             cccTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACATCGGTGACGAATGCGCCCTGt           >  1:113976/1‑69 (MQ=255)
                                             cccTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACATCGGTGACGAATGCGCCCTGt           >  1:1243583/1‑69 (MQ=255)
                                             cccTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACATCGGTGACGAATGCGCCCTGt           >  1:699279/1‑69 (MQ=255)
                                             cccTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACATCGGTGACGAATGCGCCCTGt           >  1:3176067/1‑69 (MQ=255)
                                             cccTGGCAGCGCAGGTTGGTGGTATCGGTATCGCCCCTGGCGCAAACATCGGTGACGAATGCGCCCTGt           >  1:2737077/1‑69 (MQ=255)
                                                       gcAGGTTGGCGGTATCGGTATCGCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGcca  >  1:3242865/1‑68 (MQ=255)
                                                       gcAGGTTGGCGGTATCGGTATCGCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGcca  >  1:2350532/1‑68 (MQ=255)
                                                       gcAGGTTGGCGGTATCGGTATCGACCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGcca  >  1:1941157/1‑68 (MQ=255)
                                                                |                                                          
ATGTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCCCTGGCAGCGCAGGTTGGCGGTATCGGTATCGCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCA  >  minE/775267‑775389

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