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 2,418,565 A→G 50.0% F31F (TTT→TTC)  rffM ← UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,418,5650AG50.0% ‑3.8 / 66.7 74F31F (TTT→TTC) rffMUDP‑N‑acetyl‑D‑mannosaminuronic acid transferase
Reads supporting (aligned to +/- strand):  ref base A (25/12);  new base G (20/17);  total (45/29)
Fisher's exact test for biased strand distribution p-value = 3.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.49e-01

TAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTA  >  minE/2418504‑2418628
                                                             |                                                               
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa                                                           <  1:2253291/68‑1 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa                                                           <  1:3415906/68‑1 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa                                                           >  1:999924/1‑68 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa                                                           <  1:3371381/68‑1 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa                                                           <  1:2031578/68‑1 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt                                                          >  1:474920/1‑69 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt                                                          >  1:1486916/1‑69 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt                                                          >  1:564525/1‑69 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt                                                          >  1:2755616/1‑69 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt                                                          >  1:1252000/1‑69 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt                                                          >  1:2387966/1‑69 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt                                                          >  1:1137657/1‑69 (MQ=255)
tAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGAt                                                          >  1:1119612/1‑69 (MQ=255)
 aGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa                                                           <  1:431656/67‑1 (MQ=255)
 aGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa                                                           <  1:3180696/67‑1 (MQ=255)
  gTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:2108566/60‑1 (MQ=255)
  gTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:2181808/60‑1 (MQ=255)
  gTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:3433388/60‑1 (MQ=255)
  gTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:1100669/60‑1 (MQ=255)
  gTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:1452171/60‑1 (MQ=255)
  gTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:2861989/60‑1 (MQ=255)
  gTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:1396472/60‑1 (MQ=255)
     aGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGa                                                           <  1:3167988/63‑1 (MQ=255)
       cATTTTTTCGGCTTTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:1194556/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCTCGTCAGCGAACAGATAATCGa                                                    <  1:1525369/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:2471559/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:2262926/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:3311040/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:1117336/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:982024/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:931500/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:837177/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:1990799/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:192060/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:2883425/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:1461487/68‑1 (MQ=255)
       cATTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:168006/68‑1 (MQ=255)
        aTTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:2755636/67‑1 (MQ=255)
        aTTTTTTCGGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCGAACAGATAATCGa                                                    <  1:1905300/67‑1 (MQ=255)
               cAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:1857253/47‑1 (MQ=255)
                    ttAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCat                                       <  1:605338/68‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:3308797/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:3355867/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:3409518/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:3413295/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:3126288/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:2999384/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:649807/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:1107329/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:2187484/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:1240957/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCa                                                                 <  1:2382034/40‑1 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAATCAGATAATCGAGGGCGTGCTGCATATc                                    >  1:1139179/1‑69 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGt                                              >  1:7176/1‑59 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGt                                              >  1:1866076/1‑59 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGt                                              >  1:1407153/1‑59 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGt                                              >  1:894390/1‑59 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGt                                              >  1:928711/1‑59 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCatat                                     >  1:659420/1‑68 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc                                    >  1:1777372/1‑69 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc                                    >  1:2349674/1‑69 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc                                    >  1:2236567/1‑69 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc                                    >  1:403860/1‑69 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc                                    >  1:3320247/1‑69 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc                                    >  1:3360875/1‑69 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc                                    >  1:2998012/1‑69 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATc                                    >  1:266261/1‑69 (MQ=255)
                      aaTGGCAACCAGCGTTCCCTGCTTAAGCAGCCCGTCAGCAAACAGATAATCGAGGGCGt                                              >  1:1201702/1‑59 (MQ=255)
                            aaCCAGCGTTCACTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGcca                              <  1:3004889/69‑1 (MQ=255)
                                       ccTGCTTAAGCTGACCGTCAGCGAACAGATAATCGa                                                    <  1:1919994/36‑1 (MQ=37)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:547206/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:549724/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:1408595/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:1344216/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:2028770/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:1233909/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:871707/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:1643450/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:2861585/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:2116992/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:3365236/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:2233342/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:3353058/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:3315657/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:3203072/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:2514188/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:3068562/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:2656064/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:2873701/1‑68 (MQ=255)
                                                gCTGCCCGTCAGCGAACAGATAATCGAGGGCATGCTGCATATCACGCCAACCAATCAACTGTAAGCCa           >  1:2693614/1‑68 (MQ=255)
                                                        tCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGta  <  1:654126/69‑1 (MQ=255)
                                                        tCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGta  <  1:7555/69‑1 (MQ=255)
                                                        tCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGta  <  1:2477772/69‑1 (MQ=255)
                                                             |                                                               
TAGTCAGCATTTTTTCAGCATTAATGGCAACCAGCGTTCCCTGCTTAAGCTGCCCGTCAGCAAACAGATAATCGAGGGCGTGCTGCATATCACGCCAACCAATCAACTGTAAGCCACGCAGCGTA  >  minE/2418504‑2418628

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