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 2,434,641 G→A 39.7% T86T (ACG→ACA)  gpp → guanosine pentaphosphatase/exopolyphosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,434,6410GA39.7% 45.8 / 61.9 93T86T (ACG→ACA) gppguanosine pentaphosphatase/exopolyphosphatase
Reads supporting (aligned to +/- strand):  ref base G (10/46);  new base A (34/3);  total (44/49)
Fisher's exact test for biased strand distribution p-value = 4.92e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.54e-04

TGCGCCTGTTTGCTGAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCGG  >  minE/2434574‑2434705
                                                                   |                                                                
tGCGCCTGTTTGCTGAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGt                                                                 <  1:3355834/69‑1 (MQ=255)
     cTGTTTGCTGAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGc                                                            <  1:1964768/69‑1 (MQ=255)
     cTGTTTGCTGAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGc                                                            <  1:3039430/69‑1 (MQ=255)
     cTGTTTGCTGAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGc                                                            <  1:1083084/69‑1 (MQ=255)
              gAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:1026820/69‑1 (MQ=255)
              gAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:285917/69‑1 (MQ=255)
              gAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:3155427/69‑1 (MQ=255)
              gAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:3291549/69‑1 (MQ=255)
              gAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:1217178/69‑1 (MQ=255)
              gAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:1192406/69‑1 (MQ=255)
              gAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:111505/69‑1 (MQ=255)
              gAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:577500/69‑1 (MQ=255)
               aaCGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:1643931/68‑1 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:507197/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:2397332/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:2068575/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:2026857/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:1855144/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:1000313/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:176249/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:3034275/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:1570737/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:3036048/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:1371214/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:1243651/4‑69 (MQ=255)
                             atccctccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAttt                                     >  1:2773677/4‑68 (MQ=255)
                             atccctccctcGAAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGAtttt                                    >  1:3017405/4‑69 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:3015373/53‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:965768/53‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:969817/53‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:2607852/53‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:2439320/53‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:3381289/53‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:1036561/53‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:1122109/53‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:1032970/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:218445/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:908610/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:1141638/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:2103230/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:1249770/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:2402493/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:1399987/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:1773677/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:1799570/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:2669555/69‑1 (MQ=255)
                              ttCCTCCCTCGCAAATTCGCGTTGTCGCGACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:2146678/69‑1 (MQ=255)
                              ttCATCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTc                                                   <  1:3146467/53‑1 (MQ=255)
                               tcctccCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTa                                   <  1:2066244/68‑1 (MQ=255)
                                cctccctcGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTAtt                                 >  1:590033/1‑69 (MQ=255)
                                cctccctcGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTAtt                                 >  1:558890/1‑69 (MQ=255)
                                cctccctcGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTAtt                                 >  1:2287250/1‑69 (MQ=255)
                                cctccctcGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTAtt                                 >  1:2785458/1‑69 (MQ=255)
                                cctccctcGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTAtt                                 >  1:3049204/1‑69 (MQ=255)
                                cctccctcGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTAt                                  >  1:2400961/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGc                                              >  1:2033006/1‑54 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:1275705/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:1107650/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:2579867/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:708447/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:766330/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:1139984/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:2527544/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:2758566/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:496511/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:3257031/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:2510025/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:3073843/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:2507693/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:3039970/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:1564757/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:1624603/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:2166693/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTg                                >  1:222414/1‑68 (MQ=255)
                                  tccctcGCAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGGCTATGCGGGTGATTTTATTg                                >  1:803358/1‑68 (MQ=255)
                                         cAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCa                             <  1:3272468/64‑1 (MQ=255)
                                         cAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCa                             <  1:557315/64‑1 (MQ=255)
                                         cAAATTCGCGTTGTCGCTACGGCGACATTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCa                             <  1:36137/64‑1 (MQ=255)
                                                       cGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCgg          >  1:1674797/1‑69 (MQ=255)
                                                       cGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCgg          >  1:2131389/1‑69 (MQ=255)
                                                       cGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCgg          >  1:2946277/1‑69 (MQ=255)
                                                       cGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCgg          >  1:2954405/1‑69 (MQ=255)
                                                              gCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTcc    <  1:78593/68‑1 (MQ=255)
                                                               cGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCgg  <  1:464720/69‑1 (MQ=255)
                                                               cGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCgg  <  1:2665511/69‑1 (MQ=255)
                                                               cGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCgg  <  1:419402/69‑1 (MQ=255)
                                                               cGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCgg  <  1:414848/69‑1 (MQ=255)
                                                               cGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCgg  <  1:626459/69‑1 (MQ=255)
                                                               cGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCgg  <  1:414800/69‑1 (MQ=255)
                                                               cGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCgg  <  1:708865/69‑1 (MQ=255)
                                                               cGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCgg  <  1:3418833/69‑1 (MQ=255)
                                                               cGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCgg  <  1:2197571/69‑1 (MQ=255)
                                                               cGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCgg  <  1:1649410/69‑1 (MQ=255)
                                                                   |                                                                
TGCGCCTGTTTGCTGAACGTCTGCAAGATATTCCTCCCTCGCAAATTCGCGTTGTCGCTACGGCGACGTTACGCCTTGCCGTCAATGCGGGTGATTTTATTGCCAAAGCGCAGGAAATTCTCGGTTGTCCGG  >  minE/2434574‑2434705

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