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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,581,599 T→C 31.4% K348E (AAA→GAA)  mcrC ← 5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,581,5990TC31.4% 87.2 / 61.2 70K348E (AAA→GAA) mcrC5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC
Reads supporting (aligned to +/- strand):  ref base T (13/35);  new base C (8/14);  total (21/49)
Fisher's exact test for biased strand distribution p-value = 5.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.89e-01

ATGATGAGCCGCTCCCGATGTGGTGTCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTA  >  W3110S.gb/4581537‑4581669
                                                              |                                                                      
atgatgaGCCGCTCCCGATGTGGTGTCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGata                                                                  <  1:1832328/69‑1 (MQ=255)
atgatgaGCCGCTCCCGATGTGGTGGCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATAtt                                                                <  1:2100593/71‑1 (MQ=255)
     gaGCCGCTCCCGATGTGGTGTCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATc                                                            >  1:1616497/1‑70 (MQ=255)
       gCCGCTCCCGATGTGGTGTCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTCGAGATATTCATCGaa                                                         <  1:3465209/71‑1 (MQ=255)
       gCCGCTCCCGATGTGGTGTCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTCGAGATATTCATCGaa                                                         <  1:3281528/71‑1 (MQ=255)
        ccGCTCCCGATGTGGTGTCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGaaa                                                        <  1:4031978/71‑1 (MQ=255)
              ccGATGTGGTGTCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTc                                                   <  1:3725947/70‑1 (MQ=255)
              ccGATGTGGTGTCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTc                                                   <  1:3632505/70‑1 (MQ=255)
              ccGATGTGGTGTCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCg                                                  <  1:2431745/71‑1 (MQ=255)
                  tgtgGTGTCGGGAGCGGTATTTTCTATAAAAGTTACCGCTTATTTGAGATATTCATCGaa                                                         <  1:2815548/60‑1 (MQ=255)
                      gtgtCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTc                                          >  1:2304342/1‑71 (MQ=255)
                       tgtCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTc                                                   <  1:1569898/61‑1 (MQ=255)
                         tCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGaa                                                         <  1:569567/53‑1 (MQ=255)
                         tCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGa                                                 >  1:288049/1‑61 (MQ=255)
                         tCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGa                                                 >  1:1009361/1‑61 (MQ=255)
                         tCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTg                                       <  1:2463106/71‑1 (MQ=255)
                         tCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTg                                       <  1:3236476/71‑1 (MQ=255)
                           gggAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGa                                      <  1:511199/70‑1 (MQ=255)
                           gggAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGa                                      <  1:1296927/70‑1 (MQ=255)
                                cGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCtt                                        <  1:1833107/63‑1 (MQ=255)
                                cGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCtt                                        <  1:4040175/63‑1 (MQ=255)
                                 ggTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGtata                                <  1:1481002/70‑1 (MQ=255)
                                 ggTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGta                                  <  1:3866010/68‑1 (MQ=255)
                                  gTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGt                                                    >  1:95414/1‑49 (MQ=255)
                                  gTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATac                               <  1:1179745/70‑1 (MQ=255)
                                   tATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGta                                  <  1:3837285/66‑1 (MQ=255)
                                   tATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGta                                  <  1:710170/66‑1 (MQ=255)
                                   tATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGta                                  <  1:2138538/66‑1 (MQ=255)
                                    aTTTTCTATAAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACg                            >  1:3410596/1‑71 (MQ=255)
                                     ttttCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGt                                               <  1:2244757/51‑1 (MQ=255)
                                     ttttCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGt                                               <  1:492389/51‑1 (MQ=255)
                                     ttttCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTaa                                             >  1:808010/1‑53 (MQ=255)
                                     ttttCTATAAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACgg                           >  1:3396074/1‑71 (MQ=255)
                                     ttttCTATAAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACgg                           >  1:171393/1‑71 (MQ=255)
                                     ttttCTATAAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACg                            <  1:868288/70‑1 (MQ=255)
                                       ttCTATAAAACTTACCGCTTATTTGAGATATTCATCg                                                           >  1:386401/1‑37 (MQ=255)
                                       ttCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGc                          >  1:1934040/1‑70 (MQ=255)
                                       ttCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGc                          <  1:3064705/70‑1 (MQ=255)
                                       ttCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGc                          <  1:3870050/70‑1 (MQ=255)
                                       ttCTATAAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGc                          >  1:3605459/1‑70 (MQ=255)
                                       ttCTATAAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGc                          >  1:1485526/1‑70 (MQ=255)
                                       ttCTATAAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGc                          >  1:3855067/1‑70 (MQ=255)
                                       ttCTATAAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGc                          >  1:1717611/1‑70 (MQ=255)
                                        tCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGcc                         <  1:3266342/70‑1 (MQ=255)
                                        tCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGcc                         <  1:2678560/70‑1 (MQ=255)
                                        tCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTAGAGTAATTCTTGa                                      >  1:1994368/1‑57 (MQ=255)
                                          tataAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGta                                  <  1:3861013/59‑1 (MQ=255)
                                          tataAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGta                                  <  1:2140007/59‑1 (MQ=255)
                                            taAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTaa                                             <  1:888422/46‑1 (MQ=255)
                                            taAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTaa                                             <  1:2985917/46‑1 (MQ=255)
                                            taAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTaa                                             <  1:2296835/46‑1 (MQ=255)
                                            taAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTaa                                             <  1:1363466/46‑1 (MQ=255)
                                            taAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCtt                                        <  1:3065827/51‑1 (MQ=255)
                                            taAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCtt                                        <  1:364809/51‑1 (MQ=255)
                                            taAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCAt                       <  1:1657415/68‑1 (MQ=255)
                                            taAAACTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCAt                       <  1:971310/68‑1 (MQ=255)
                                             aataCTTACGGCTTTTTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTc                     <  1:1674418/66‑1 (MQ=255)
                                              aaaCTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTcc                    >  1:1468420/1‑69 (MQ=255)
                                                 cTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTaa                                             >  1:796864/1‑41 (MQ=255)
                                                 cTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGAcc               >  1:2251016/1‑71 (MQ=255)
                                                 cTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGAcc               >  1:3577681/1‑71 (MQ=255)
                                                 cTTACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGAcc               >  1:992982/1‑71 (MQ=255)
                                                  ttACCGCTTATTCGAGATATTCATCGAAAATGTCGAGTAATTCtt                                        <  1:4061871/45‑1 (MQ=255)
                                                    aCCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTa             <  1:3798584/70‑1 (MQ=255)
                                                    aCCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTa             <  1:3070234/70‑1 (MQ=255)
                                                     ccGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTaa            <  1:1040763/70‑1 (MQ=255)
                                                     ccGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTa             <  1:132907/69‑1 (MQ=255)
                                                       gCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATg                                    <  1:841419/44‑1 (MQ=255)
                                                          tATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTa             <  1:464091/64‑1 (MQ=255)
                                                          tATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTa             <  1:2058598/64‑1 (MQ=255)
                                                            tttGAGATATTCATCGAAAATGTCGAGTAATTCTTGa                                      <  1:177159/37‑1 (MQ=255)
                                                            tttGAGATATTCATCGAAAATGTCGAGTAATTCTTGATg                                    <  1:1157548/39‑1 (MQ=255)
                                                            tttGAGATATTCATCGAAAATGTCGAGTAATTCTTGATg                                    <  1:1066291/39‑1 (MQ=255)
                                                            tttGAGATATTCATCGAAAATGTCGAGTAATTCTTGATg                                    <  1:4063546/39‑1 (MQ=255)
                                                            tttGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACgg    <  1:1203056/71‑1 (MQ=255)
                                                             ttGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACgg    <  1:3298041/70‑1 (MQ=255)
                                                              tGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTa  >  1:3746002/1‑71 (MQ=255)
                                                              tGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTa  >  1:437912/1‑71 (MQ=255)
                                                              tGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTa  >  1:12414/1‑71 (MQ=255)
                                                              |                                                                      
ATGATGAGCCGCTCCCGATGTGGTGTCGGGAGCGGTATTTTCTATAAAACTTACCGCTTATTTGAGATATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTA  >  W3110S.gb/4581537‑4581669

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