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 352,455 C→T 33.6% Q187Q (CAG→CAA)  lpxH ← UDP‑2,3‑diacylglucosamine pyrophosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE352,4550CT33.6% 64.8 / 44.3 83Q187Q (CAG→CAA) lpxHUDP‑2,3‑diacylglucosamine pyrophosphatase
Reads supporting (aligned to +/- strand):  ref base C (25/30);  new base T (15/13);  total (40/43)
Fisher's exact test for biased strand distribution p-value = 4.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

TGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGATTTAC  >  minE/352390‑352519
                                                                 |                                                                
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:233464/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:355117/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:368519/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:2161243/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:1703525/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:2971904/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:1584228/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:1572293/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:2911171/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:660713/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:1338909/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:689433/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:824120/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:1125509/1‑69 (MQ=255)
tGCTGATTGGCGATAAGTTCATGCACCGACGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGa                                                               >  1:187892/1‑69 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:2351003/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:1042087/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:2392042/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:2601780/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:258635/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:2145286/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:2050340/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:2453035/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:2579340/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:1836907/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:807502/69‑1 (MQ=255)
             tAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:662418/69‑1 (MQ=255)
             tAAGTTCATGCAACGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACTTGATGTTTTTCCATCg                                                  <  1:1445575/69‑1 (MQ=255)
              aaGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGc                                                 <  1:3227603/69‑1 (MQ=255)
              aaGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGc                                                 <  1:505690/69‑1 (MQ=255)
              aaGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGc                                                 <  1:1726168/69‑1 (MQ=255)
              aaGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGc                                                 <  1:1120719/69‑1 (MQ=255)
              aaGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGc                                                 <  1:548842/69‑1 (MQ=255)
                 ttCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACt                                              >  1:2031118/1‑69 (MQ=255)
                 ttCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACt                                              >  1:2548919/1‑69 (MQ=255)
                 ttCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACt                                              >  1:2482277/1‑69 (MQ=255)
                 ttCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACt                                              >  1:1687941/1‑69 (MQ=255)
                 ttCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACt                                              >  1:3225051/1‑69 (MQ=255)
                 ttCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATAGCACt                                              >  1:302952/1‑69 (MQ=255)
                 ttCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCAATCGCACt                                              >  1:2844791/1‑69 (MQ=255)
                 ttCATGCACCGACGGGCGATGGGTATGACCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACt                                              >  1:101046/1‑69 (MQ=255)
                 ttCATGAACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACt                                              >  1:1447/1‑69 (MQ=255)
                                          tGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTcc                     >  1:990674/1‑69 (MQ=255)
                                          tGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTcc                     >  1:118268/1‑69 (MQ=255)
                                          tGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTcc                     >  1:2010698/1‑69 (MQ=255)
                                          tGCCAGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTcc                     >  1:1271611/1‑69 (MQ=255)
                                            cccGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCa                    >  1:559990/1‑68 (MQ=255)
                                              cGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATg                  <  1:2316138/68‑1 (MQ=255)
                                                  gATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATg                  >  1:1125830/1‑64 (MQ=255)
                                                  gATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATc               >  1:2558225/1‑67 (MQ=255)
                                                  gATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATc               >  1:1541206/1‑67 (MQ=255)
                                                  gATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATc               >  1:1866575/1‑67 (MQ=255)
                                                  gATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATc               >  1:2181500/1‑67 (MQ=255)
                                                          aTTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAtt     <  1:591112/69‑1 (MQ=255)
                                                          aTTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAtt     <  1:2950927/69‑1 (MQ=255)
                                                          aTTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAtt     <  1:3014401/69‑1 (MQ=255)
                                                          aTTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAtt     <  1:310148/69‑1 (MQ=255)
                                                          aTTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAtt     <  1:1395545/69‑1 (MQ=255)
                                                          aTTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAtt     <  1:2378718/69‑1 (MQ=255)
                                                          aTTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAtt     <  1:3391095/69‑1 (MQ=255)
                                                          aTTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAtt     <  1:3407288/69‑1 (MQ=255)
                                                           ttGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:2212914/69‑1 (MQ=255)
                                                           ttGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:2712135/69‑1 (MQ=255)
                                                           ttGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAtt     <  1:633852/68‑1 (MQ=255)
                                                            tGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGATTTa   >  1:446210/1‑69 (MQ=255)
                                                            tGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGATTTa   >  1:1912277/1‑69 (MQ=255)
                                                            tGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGATTTa   >  1:769863/1‑69 (MQ=255)
                                                            tGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGATTTa   >  1:2410964/1‑69 (MQ=255)
                                                            tGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGATTTa   >  1:3002980/1‑69 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:2497992/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:414325/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:1151851/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:2520999/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:1117242/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:628796/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:2589283/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:1947943/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:2801302/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:3218079/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:3204245/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:2319048/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGAttt    <  1:2961581/67‑1 (MQ=255)
                                                             gCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGATTTAc  >  1:2452455/1‑69 (MQ=255)
                                                                 |                                                                
TGCTGATTGGCGATAAGTTCATGCACCGCCGGGCGATGGGTATGCCCGTGGATCAGCCATTGCACCTGATGTTTTTCCATCGCACTGACCACCGCGTTTTGGTTAACGTCCATGATCGCCAGCGATTTAC  >  minE/352390‑352519

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