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 260,171 T→C 43.4% P104P (CCA→CCG)  tsx ← nucleoside channel, receptor of phage T6 and colicin K

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE260,1710TC43.4% 25.7 / 83.4 106P104P (CCA→CCG) tsxnucleoside channel, receptor of phage T6 and colicin K
Reads supporting (aligned to +/- strand):  ref base T (26/34);  new base C (11/35);  total (37/69)
Fisher's exact test for biased strand distribution p-value = 4.23e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.18e-01

Only 100 of 106 total aligned reads displayed.

ACCACTCTTTGAACGGACCGAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATACCTTTAGCATCGGAGTT  >  minE/260110‑260230
                                                             |                                                           
aCCACTCTTTGAACGGACCGAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAACCGTGGTTCGa                                                      >  1:2494092/1‑69 (MQ=255)
aCCACTCTTTGAACGGACCGAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGa                                                      >  1:1883875/1‑69 (MQ=255)
aCCACTCTTTGAACGGACCGAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGa                                                      >  1:2330711/1‑69 (MQ=255)
aCCACTCTTTGAACGGACCGAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGa                                                      >  1:2997326/1‑69 (MQ=255)
aCCACTCTTTGAACGGACCGAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGa                                                      >  1:2956155/1‑69 (MQ=255)
aCCACTCTTTGAACGGACCGAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGa                                                      >  1:2799711/1‑69 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:2742251/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:203437/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:2053986/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:1921938/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:2407609/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:2583310/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:2702921/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:168918/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:430296/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:90608/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:617650/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:449847/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:371031/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:3288073/69‑1 (MQ=255)
 ccACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:2915837/69‑1 (MQ=255)
  cACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:388624/68‑1 (MQ=255)
  cACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:519589/68‑1 (MQ=255)
  cACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:1623907/68‑1 (MQ=255)
  cACTCTTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:1980913/68‑1 (MQ=255)
     tctTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGATTTc                                                  >  1:2576087/1‑68 (MQ=255)
     tctTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGATTTc                                                  >  1:2838634/1‑68 (MQ=255)
     tctTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGATTTc                                                  >  1:2324120/1‑68 (MQ=255)
     tctTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGATTTc                                                  >  1:2262480/1‑68 (MQ=255)
     tctTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGATTTc                                                  >  1:618893/1‑68 (MQ=255)
     tctTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGATTTc                                                  >  1:9905/1‑68 (MQ=255)
     tctTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGATTTc                                                  >  1:1066145/1‑68 (MQ=255)
     tctTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGATTTc                                                  >  1:1212373/1‑68 (MQ=255)
     tctTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGATTTc                                                  >  1:1354297/1‑68 (MQ=255)
     tctTTGAACGGACCAAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGATTTc                                                  >  1:1783649/1‑68 (MQ=255)
      ctTTGAACGGACCGAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTcc                                                 >  1:897619/1‑68 (MQ=255)
                             tCAGTATTGGTCAGCTTGTCGATGTAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGt                           >  1:871635/1‑67 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:2050461/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:1017944/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:824200/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:772859/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:3349357/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:3230803/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:3228915/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:3086235/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:2922326/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:2582887/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:1999965/40‑1 (MQ=255)
                              cAGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:1822967/40‑1 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATCAACAGCGGAGAACCGTGGTTCCa                       <  1:2904915/69‑1 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCg                                       >  1:1294096/1‑53 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCg                                       >  1:3435705/1‑53 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCg                                       >  1:3280298/1‑53 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCg                                       >  1:537786/1‑53 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCg                                       >  1:115271/1‑53 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCg                                       >  1:2416765/1‑53 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCg                                       >  1:2249316/1‑53 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCg                                       >  1:902695/1‑53 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCg                                       >  1:2130064/1‑53 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCa                       <  1:789673/69‑1 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCa                       <  1:124394/69‑1 (MQ=255)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCTAt                                                     <  1:3168145/39‑1 (MQ=37)
                               aGTATTGGTCAGCTTGTCGATGGAGAAACGCGGTTCGAt                                                     <  1:2796242/39‑1 (MQ=255)
                                 tATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGa                     <  1:2929155/69‑1 (MQ=255)
                                 tATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGa                     <  1:2932896/69‑1 (MQ=255)
                                 tATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGa                     <  1:3044423/69‑1 (MQ=255)
                                   ttGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:1472838/69‑1 (MQ=255)
                                   ttGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:349724/69‑1 (MQ=255)
                                   ttGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:1214687/69‑1 (MQ=255)
                                   ttGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:1349274/69‑1 (MQ=255)
                                   ttGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:264656/69‑1 (MQ=255)
                                   ttGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:1840798/69‑1 (MQ=255)
                                   ttGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:223395/69‑1 (MQ=255)
                                   ttGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:142221/69‑1 (MQ=255)
                                   ttGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:835181/69‑1 (MQ=255)
                                    tGGGCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:679629/68‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTc                                                  <  1:781704/36‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTc                                                  <  1:945951/36‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTc                                                  <  1:2046726/36‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTc                                                  <  1:33042/36‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTc                                                  <  1:2586328/36‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTc                                                  <  1:326130/36‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTc                                                  <  1:2358902/36‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTc                                                  <  1:143074/36‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTc                                                  <  1:3078010/36‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:1229231/67‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   >  1:1789574/1‑67 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:202060/67‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:3160113/67‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   >  1:1868020/1‑67 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACCTGGTTCGATTTc                                                  <  1:1733255/36‑1 (MQ=255)
                                     ggTCAGCTTGTCGATGGAGAAACCTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATa                   <  1:1919593/67‑1 (MQ=255)
                                             tGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATACCTTTAGCAt         >  1:700614/1‑69 (MQ=255)
                                                 gATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATACCTTTAGCATCgg      <  1:2464877/68‑1 (MQ=255)
                                                          aCGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATACCTTTAGCATCGGAGtt  >  1:2956129/1‑63 (MQ=255)
                                                          aCGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATACCTTTAGCATCGGAGtt  >  1:817076/1‑63 (MQ=255)
                                                          aCGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATACCTTTAGCATCGGAGtt  >  1:2883775/1‑63 (MQ=255)
                                                          aCGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATACCTTTAGCATCGGAGtt  >  1:1487907/1‑63 (MQ=255)
                                                          aCGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATACCTTTAGCATCGGAGtt  >  1:1542278/1‑63 (MQ=255)
                                                          aCGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATACCTTTAGCATCGGAGtt  >  1:1164003/1‑63 (MQ=255)
                                                             |                                                           
ACCACTCTTTGAACGGACCGAAGCTAAGGTCAGTATTGGTCAGCTTGTCGATGGAGAAACGTGGTTCGATTTCCATAAACAGCGGAGAACCGTGGTTCCAGATACCTTTAGCATCGGAGTT  >  minE/260110‑260230

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