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 1,683,045 G→A 62.0% G643G (GGC→GGT)  yfhM ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,683,0450GA62.0% 34.7 / 45.1 71G643G (GGC→GGT) yfhMconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (23/4);  new base A (5/39);  total (28/43)
Fisher's exact test for biased strand distribution p-value = 4.21e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01

CAAGCCCGACACGGCTTTTTTCACGCCTTGCGCATCGCTATAAACGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGATTTCGAGGCG  >  minE/1682979‑1683111
                                                                  |                                                                  
cAAGCTCGACACGGCTTTTTTCACGCCTTGCGCATCGCTATAAACGATGTCAAAAGCGGCGTTACTAcc                                                                  >  1:1202227/1‑69 (MQ=255)
cAAGCTCGACACGGCTTTTTTCACGCCTTGCGCATCGCTATAAACGATGTCAAAAGCGGCGTTACTAcc                                                                  >  1:2372161/1‑69 (MQ=255)
cAAGCTCGACACGGCTTTTTTCACGCCTTGCGCATCGCTATAAACGATGTCAAAAGCGGCGTTACTAcc                                                                  >  1:1519365/1‑69 (MQ=255)
cAAGCTCGACACGGCTTTTTTCACGCCTTGCGCATCGCTATAAACGATGTCAAAAGCGGCGTTACTAcc                                                                  >  1:2397876/1‑69 (MQ=255)
cAAGCTCGACACGGCTTTTTTCACGCCTTGCGCATCGCTATAAACGATGTCAAAAGCGGCGTTACTAcc                                                                  >  1:3393129/1‑69 (MQ=255)
  aGCCCGACACGGCTTTTTTCACGCCTTGCGCATCGCTATAAACGATGTCAAAAGCGGCGTTACTGcc                                                                  <  1:444012/67‑1 (MQ=255)
  aGCCCGACACGGCTTTTTTCACGCCTTGCGCATCGCTATAAACGATGTCAAAAGCGGCGTTACTGcc                                                                  <  1:1857362/67‑1 (MQ=255)
  aGCCCGACACGGCTTTTTTCACGCCTTGCGCATCGCTATAAACGATGTCAAAAGCGGCGTTACTGCCtt                                                                <  1:233829/69‑1 (MQ=255)
                                    gCTATAAACGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGt                              >  1:79924/1‑69 (MQ=255)
                                    gCTATAAACGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGt                              >  1:527124/1‑69 (MQ=255)
                                    gCTATAAACGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGt                              >  1:2142719/1‑69 (MQ=255)
                                    gCTATAAACGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGt                              >  1:868462/1‑69 (MQ=255)
                                    gCTATAAACGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGt                              >  1:875482/1‑69 (MQ=255)
                                    gCTATAAACGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGt                              >  1:3316359/1‑69 (MQ=255)
                                    gCTATAAAAGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGt                              >  1:1379929/1‑69 (MQ=255)
                                          aaCGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATa                        >  1:1188591/1‑69 (MQ=255)
                                          aaCGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATa                        >  1:3153878/1‑69 (MQ=255)
                                             gATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAAt                      >  1:357810/1‑68 (MQ=255)
                                             gATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAAt                      >  1:792164/1‑68 (MQ=255)
                                             gATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAAt                      >  1:2594032/1‑68 (MQ=255)
                                             gATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAAt                      >  1:2529906/1‑68 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:3266887/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:3013886/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:3031581/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:3148431/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:961808/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:3162864/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:317709/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:616086/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:897311/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:3436193/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:76790/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:735993/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:734481/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:621744/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:1237483/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:2718891/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:1540530/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:2682254/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:2510281/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:2483972/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:2395349/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:2428572/69‑1 (MQ=255)
                                                          gcgTTACTACCTTCATCAACAATCGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:1166086/69‑1 (MQ=255)
                                                           cgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:562521/68‑1 (MQ=255)
                                                           cgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:889335/68‑1 (MQ=255)
                                                           cgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:1820982/68‑1 (MQ=255)
                                                           cgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:2687100/68‑1 (MQ=255)
                                                           cgTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTc        <  1:2836517/68‑1 (MQ=255)
                                                            gTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:2401662/69‑1 (MQ=255)
                                                            gTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:199358/69‑1 (MQ=255)
                                                            gTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:2059769/69‑1 (MQ=255)
                                                            gTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:221487/69‑1 (MQ=255)
                                                            gTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:2975905/69‑1 (MQ=255)
                                                            gTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:933790/69‑1 (MQ=255)
                                                            gTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:2412335/69‑1 (MQ=255)
                                                            gTTACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:392885/69‑1 (MQ=255)
                                                             ttACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGAt           >  1:2733207/1‑63 (MQ=255)
                                                             ttACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGATTTCGAg     >  1:598412/1‑69 (MQ=255)
                                                             ttACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGATTTCGAg     >  1:235686/1‑69 (MQ=255)
                                                             ttACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:2287587/68‑1 (MQ=255)
                                                             ttACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:825112/68‑1 (MQ=255)
                                                             ttACTACCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCGGTGCGATAATCGTAAACCGATTTCGa      <  1:863648/68‑1 (MQ=255)
                                                               aCTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTc                                 >  1:1202298/1‑39 (MQ=255)
                                                               aCTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTc                                 >  1:1764303/1‑39 (MQ=255)
                                                               aCTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGATTTCGAgg    >  1:3023857/1‑68 (MQ=255)
                                                               aCTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGATTTCGAgg    >  1:2004817/1‑68 (MQ=255)
                                                               aCTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGATTTCGAgg    >  1:614611/1‑68 (MQ=255)
                                                               aCTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGATTTCGAgg    >  1:417087/1‑68 (MQ=255)
                                                               aCTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGATTTCGAg     >  1:3309337/1‑67 (MQ=255)
                                                                 tGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGATTTCGAGGCg  <  1:3342086/68‑1 (MQ=255)
                                                                  |                                                                  
CAAGCCCGACACGGCTTTTTTCACGCCTTGCGCATCGCTATAAACGATGTCAAAAGCGGCGTTACTGCCTTCATCAACAATGGGCTGTTTCACCGTGCTGTCAGTACGATAATCGTAAACCGATTTCGAGGCG  >  minE/1682979‑1683111

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