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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 836,467 C→T 22.8% T395T (ACC→ACT) ‡ narH → nitrate reductase 1, beta (Fe‑S) subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE836,4670CT22.8% 104.9 / 23.9 57T395T (ACC→ACT) ‡narHnitrate reductase 1, beta (Fe‑S) subunit
Reads supporting (aligned to +/- strand):  ref base C (25/19);  new base T (7/6);  total (32/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAGCAACGGCATTCTGCCAGACGTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTATGCTGGCGATGCGTCATTACAAACGTGCT  >  minE/836397‑836536
                                                                      |                                                                     
gTAGCAACGGCATTCTGCCAGACGTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGAcc                                                                       >  1:1523098/1‑71 (MQ=255)
   gCAACGGCATTCTGCCAGACGTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGAccgcc                                                                    >  1:2224747/1‑71 (MQ=255)
     aaCGGCATTCTGCCAGACGTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCgg                                                                  >  1:3747422/1‑71 (MQ=255)
      aCGGCATTCTGCCAGACGTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGt                                                                 >  1:28786/1‑71 (MQ=255)
      aCGGCATTCTGCCAGACGTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGt                                                                 <  1:1931873/71‑1 (MQ=255)
             tCTGCCAGACGTCAAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATAcc                                                           >  1:3861722/1‑70 (MQ=255)
               tGCCAGACGTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCaaa                                                        >  1:2621459/1‑71 (MQ=255)
                   aGACGTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCgg                                                    <  1:2195677/71‑1 (MQ=255)
                    gACGTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGt                                                   <  1:386904/71‑1 (MQ=255)
                       gTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACt                                                >  1:2737099/1‑71 (MQ=255)
                       gTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACt                                                >  1:2060746/1‑71 (MQ=255)
                        tCGAAAGCCTGCGTATTCCGGTGCAATATCTCGCCAATATGTTGAGTGCCggc                                                                 <  1:4324141/53‑2 (MQ=255)
                        tCGAAAGCCTGCGTATTCCGGTGCAATATCTCGCCAATATGTTGAGTGCCggc                                                                 <  1:4330503/53‑2 (MQ=255)
                         cGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTgc                                              >  1:3698793/1‑71 (MQ=255)
                         cGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTgc                                              >  1:3473738/1‑71 (MQ=255)
                          gAAAGCCTGCGTATTCCGGTGCAATATCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTa                                                  >  1:1249682/1‑66 (MQ=255)
                             aGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTgcgcg                                           >  1:1105263/1‑70 (MQ=255)
                                cTGCGTATTCCGGTGCAATATCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTACTGCGGGCGCt                                       <  1:2254244/71‑1 (MQ=255)
                                cTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACt                                       <  1:2687358/71‑1 (MQ=255)
                                   cGTATTCCGGTGCAATATCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTACTGCGGGCGCTGa                                     <  1:4432431/70‑1 (MQ=255)
                                   cGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGaa                                    <  1:4110428/71‑1 (MQ=255)
                                   cGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGa                                     >  1:3630906/1‑70 (MQ=255)
                                    gTATTCCGGTGCAATATCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTACTGCGGGCGCTGaa                                    >  1:1837881/1‑70 (MQ=255)
                                     tATTCCGGTGCAATATCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTACTGCGGGCGCt                                       <  1:1188187/66‑1 (MQ=255)
                                     tATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACt                                                <  1:1475079/57‑1 (MQ=255)
                                       ttCCGGTGCAATATCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTACTGCGGGCGCTGAAACg                                 <  1:1596027/70‑1 (MQ=255)
                                       ttCCGGTGCAATATCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTACTGCGGGCGCTGAAACg                                 >  1:401318/1‑70 (MQ=255)
                                        tCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTa                               >  1:65595/1‑71 (MQ=255)
                                         ccGGTGCAATATCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTACTGCGGGCGCTGAAACGGAt                              >  1:1989129/1‑71 (MQ=255)
                                         ccGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTAt                              >  1:4710526/1‑71 (MQ=255)
                                         ccGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTAt                              >  1:1161640/1‑71 (MQ=255)
                                            gTACAGTATCTGGCGAATCTGCTGACCGCCGGAGATACCAAACCGGTACTGCGCGCACTGAAACGTATGCt                           <  1:537934/71‑1 (MQ=255)
                                              aCAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTATGCt                           <  1:1362446/69‑1 (MQ=255)
                                               caatATCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTACTGCGGGCGCTGAAACGGATGATGGc                        >  1:982427/4‑71 (MQ=255)
                                                aatATCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTACTGCGGGCGCTGAAACGGATGATGGc                        >  1:5160913/3‑70 (MQ=255)
                                                 gTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCa                                         >  1:4812093/1‑52 (MQ=255)
                                                 gTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCa                                         >  1:603611/1‑52 (MQ=255)
                                                 gTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCa                                         >  1:2672883/1‑52 (MQ=255)
                                                  tATCTGGCGAATCTGCTGACCGCCGGTGATACCAAAc                                                       <  1:4700042/37‑1 (MQ=255)
                                                  tATCTGGCGAATCTGCTGACCGCCGGTGATACCAAAc                                                       <  1:3942951/37‑1 (MQ=255)
                                                  tATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTa                                                  >  1:5315952/1‑42 (MQ=255)
                                                   aTCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGa                                     >  1:236465/1‑54 (MQ=255)
                                                   aTCTCGCCAATATGTTGAGTGCCGGCGATACCGGTCCGGTACTGCGGGCGCTGAAACGGATGATGGCGATg                    >  1:295549/1‑71 (MQ=255)
                                                    tCTGGCGAATCTGCTGACCGCCGGTGATACCAAAc                                                       <  1:1542139/35‑1 (MQ=255)
                                                      tGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGa                                     <  1:1838486/51‑1 (MQ=255)
                                                      tGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGa                                     <  1:1812489/51‑1 (MQ=255)
                                                      tGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGa                                     <  1:727777/51‑1 (MQ=255)
                                                           aaTCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGaaa                                   >  1:5265714/1‑48 (MQ=255)
                                                           aaTCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGa                                     <  1:1351984/46‑1 (MQ=255)
                                                               tgctgACCGCCGGTGATACCAAACCGGTACTGCTCGCACTGa                                     <  1:4878885/42‑1 (MQ=255)
                                                               tgctgACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGa                                     <  1:4524877/42‑1 (MQ=255)
                                                               tgctgACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGa                                     <  1:2862653/42‑1 (MQ=255)
                                                                 ctgACCGCCGGTTATACCAAACCGGTACTGCGCGCACTGAAACGTa                               >  1:4896566/1‑46 (MQ=255)
                                                                 ctgACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTa                               >  1:5451852/1‑46 (MQ=255)
                                                                 ctgACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTATGCTGGCGATGCGTCATTACAAAc       <  1:3179718/70‑1 (MQ=255)
                                                                 ctgACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTATGCTGGCGATGCGTCATTACAAACg      >  1:563775/1‑71 (MQ=255)
                                                                  tgACCGCCGGTGATACCAAACCGGTACTGCGTGCACTGAAACGTATGCTGGCGATGCGTCAt              >  1:2935420/1‑62 (MQ=255)
                                                                  tgACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTATGCTGGCGATGCGTCAt              >  1:2774006/1‑62 (MQ=255)
                                                                  tgACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTATGCTGGCGATGCGTCAt              >  1:1198279/1‑62 (MQ=255)
                                                                      cgccgGTGATACCAAACCGGTACTGCGCGCACTGAAACGTATGCTGGCGATGCGTCATTACAAACGTGCt  >  1:3694536/1‑70 (MQ=255)
                                                                      |                                                                     
GTAGCAACGGCATTCTGCCAGACGTCGAAAGCCTGCGTATTCCGGTACAGTATCTGGCGAATCTGCTGACCGCCGGTGATACCAAACCGGTACTGCGCGCACTGAAACGTATGCTGGCGATGCGTCATTACAAACGTGCT  >  minE/836397‑836536

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