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 1,402,727 C→T 42.6% G190G (GGC→GGT)  rtn → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,402,7270CT42.6% 27.9 / 59.9 82G190G (GGC→GGT) rtnconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (24/23);  new base T (16/19);  total (40/42)
Fisher's exact test for biased strand distribution p-value = 6.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.47e-01

CCTGACGCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTAACCGACATGC  >  minE/1402661‑1402788
                                                                  |                                                             
ccTGACGCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCaa                                                             <  1:1737173/69‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTGATACTg                                                        <  1:2414664/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:2588546/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:3289016/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:2341530/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:2310168/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:50444/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:2154716/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:2114021/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:637443/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:1903112/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:1712441/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:822539/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:1637860/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:3063781/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:3033443/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:2668567/68‑1 (MQ=255)
      gCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTAAGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:1577903/68‑1 (MQ=255)
       ccTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:27094/67‑1 (MQ=255)
             ctctTTTATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCt                                                >  1:531938/1‑69 (MQ=255)
             ctctTTTATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCt                                                >  1:747063/1‑69 (MQ=255)
             ctctTTTATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCt                                                >  1:27067/1‑69 (MQ=255)
             ctctTTTATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCt                                                >  1:2973538/1‑69 (MQ=255)
             ctctTTTATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCt                                                >  1:2866845/1‑69 (MQ=255)
             ctctTTTATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCt                                                >  1:1816047/1‑69 (MQ=255)
                ttttATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAAt                                                            >  1:2098915/1‑54 (MQ=255)
                ttttATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAAt                                                            <  1:3208549/54‑1 (MQ=255)
                ttttATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAAt                                                            >  1:2346778/1‑54 (MQ=255)
                          cACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTttctt                                      >  1:2085123/1‑66 (MQ=255)
                          cACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:1456828/1‑69 (MQ=255)
                          cACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:210059/1‑69 (MQ=255)
                          cACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:372953/1‑69 (MQ=255)
                                   aaGATTACGATGGCCTAGCCCTCATTATTGGTAATACTg                                                        <  1:2714015/39‑1 (MQ=255)
                                       ttACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACg                       >  1:2602791/1‑68 (MQ=255)
                                         aCGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTa                    <  1:3182905/69‑1 (MQ=255)
                                         aCGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTa                    <  1:3067882/69‑1 (MQ=255)
                                         aCGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTa                    <  1:3132583/69‑1 (MQ=255)
                                         aCGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTa                    <  1:2288237/69‑1 (MQ=255)
                                         aCGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTa                    <  1:2031900/69‑1 (MQ=255)
                                         aCGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTa                    <  1:1964311/69‑1 (MQ=255)
                                         aCGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTa                    <  1:1390713/69‑1 (MQ=255)
                                          cGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTa                    <  1:457057/68‑1 (MQ=255)
                                          cGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTa                    <  1:3020707/68‑1 (MQ=255)
                                            aTGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAAAGTTa                    <  1:3322039/66‑1 (MQ=255)
                                             tGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGa                <  1:983614/69‑1 (MQ=255)
                                             tGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGa                <  1:2190158/69‑1 (MQ=255)
                                             tGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGa                <  1:273852/69‑1 (MQ=255)
                                             tGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGa                <  1:3238939/69‑1 (MQ=255)
                                             tGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGa                <  1:699929/69‑1 (MQ=255)
                                              ggCGTCGCCCTCATTATTGGCAATACTGCGCTATc                                                 >  1:2710500/1‑35 (MQ=255)
                                              ggCGTCGCCCTCATTATTGGCAATACTGCGCTATc                                                 >  1:717013/1‑35 (MQ=255)
                                              ggCGTCGCCCTCATTATTGGCAATACTGCGCTATc                                                 >  1:702622/1‑35 (MQ=255)
                                              ggCGTCGCCCTCATTATTGGCAATACTGCGCTATc                                                 >  1:3257908/1‑35 (MQ=255)
                                              ggCGTCGCCCTCATTATTGGCAATACTGCGCTATc                                                 >  1:3430527/1‑35 (MQ=255)
                                              ggCGTCGCCCTCATTATTGGCAATACTGCGCTATc                                                 >  1:2266095/1‑35 (MQ=255)
                                               gCGTCTCCCTCATTATTGGCAATACTGCGCTATCTACCTTttc                                        >  1:2135101/1‑43 (MQ=255)
                                               gCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGaa               >  1:2779450/1‑68 (MQ=255)
                                               gCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGaa               >  1:550083/1‑68 (MQ=255)
                                               gCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGaa               >  1:2758325/1‑68 (MQ=255)
                                               gCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGaa               >  1:3238862/1‑68 (MQ=255)
                                                      ccTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTAACCGa       <  1:864435/69‑1 (MQ=255)
                                                      ccTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTAACCGa       <  1:851745/69‑1 (MQ=255)
                                                      ccTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTAACCGa       <  1:1264674/69‑1 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTttcttc                                     >  1:1906022/1‑38 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:1230902/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:977744/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:971163/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:1357429/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:1370872/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:1724887/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:3002453/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:321969/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:2174028/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:2268439/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:36489/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:2474510/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:3334198/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:2565808/1‑40 (MQ=255)
                                                       cTCATTATTGGTAATACTGCGCTATCTACCTTTTCTTCAc                                   >  1:268062/1‑40 (MQ=255)
                                                        tCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTa            <  1:1007828/62‑1 (MQ=255)
                                                            tattGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTAACCGACATGc  <  1:1293500/68‑1 (MQ=255)
                                                             attGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTAACCGACATGc  <  1:659367/67‑1 (MQ=255)
                                                                  |                                                             
CCTGACGCCTTCACTCTTTTATAGTTCACGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTAACCGACATGC  >  minE/1402661‑1402788

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