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 F17 I0 R2 278 43.2 2215644 94.6% 2095999 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,516,656 C→T 31.7% A102T (GCT→ACT)  trmH ← tRNA (Guanosine‑2'‑O‑)‑methyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,516,6560CT31.7% 116.9 / 68.5 82A102T (GCT→ACT) trmHtRNA (Guanosine‑2'‑O‑)‑methyltransferase
Reads supporting (aligned to +/- strand):  ref base C (30/26);  new base T (13/13);  total (43/39)
Fisher's exact test for biased strand distribution p-value = 8.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCCCGTTTTCTCCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGATGAGCGACGGCATCGCC  >  minE/2516587‑2516722
                                                                     |                                                                  
tGCCCGTTTTCTCCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCg                                                                   >  1:217726/1‑71 (MQ=255)
  cccGTTTTCTCCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGtt                                                                 <  1:351389/71‑1 (MQ=255)
    cGTTTTCTCCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTAt                                                               >  1:572162/1‑71 (MQ=255)
       tttCTCCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTAt                                                               >  1:769719/1‑68 (MQ=255)
       ttgctcCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTAAt                                                               >  1:947769/4‑68 (MQ=255)
        ttCTCCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAg                                                            >  1:224344/1‑70 (MQ=255)
        ttCTCCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAg                                                            >  1:315048/1‑70 (MQ=255)
        ttCTCCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAg                                                            >  1:818588/1‑70 (MQ=255)
        ttCTCCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAg                                                            >  1:455176/1‑70 (MQ=255)
          ctcCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGaa                                                          <  1:1441976/70‑1 (MQ=255)
            ccTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGa                                                           >  1:357079/1‑67 (MQ=255)
             cTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGaaa                                                         <  1:941523/68‑1 (MQ=255)
             cTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGaaa                                                         <  1:681723/68‑1 (MQ=255)
             cTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAg                                                        <  1:59018/69‑1 (MQ=255)
             cTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAg                                                        <  1:1330478/69‑1 (MQ=255)
             cTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAg                                                        <  1:65427/69‑1 (MQ=255)
             cTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAg                                                        <  1:1057297/69‑1 (MQ=255)
              tGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGaaa                                                         <  1:1446434/67‑1 (MQ=255)
                  ccATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGt                                                  <  1:247694/70‑1 (MQ=255)
                   cATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGtt                                                                 <  1:1316309/54‑1 (MQ=255)
                   cATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGaaa                                                         <  1:1800844/62‑1 (MQ=255)
                    aTCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGc                                               >  1:437563/1‑71 (MQ=255)
                      cAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGc                                               >  1:819600/1‑69 (MQ=255)
                      cAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGt                                                                  >  1:784542/1‑50 (MQ=255)
                      cAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGt                                                                  >  1:781943/1‑50 (MQ=255)
                      cAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGt                                                                  >  1:125261/1‑50 (MQ=255)
                      cAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGc                                               >  1:2123479/1‑69 (MQ=255)
                      cAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGc                                               >  1:1995904/1‑69 (MQ=255)
                      cAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGc                                               >  1:2030874/1‑69 (MQ=255)
                       aaaaTGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCTACAGCGTTATCAGAAAGATGGGTTGCCAg                                            <  1:1423733/71‑1 (MQ=255)
                       aaaaTGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGc                                               >  1:2153693/1‑68 (MQ=255)
                       aaaaTGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGc                                               >  1:668996/1‑68 (MQ=255)
                        aaaTGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGa                                           <  1:1129427/71‑1 (MQ=255)
                        aaaTGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGa                                           <  1:329439/71‑1 (MQ=255)
                         aaTGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGa                                           <  1:731685/70‑1 (MQ=255)
                          aTGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGa                                                       >  1:2205129/1‑57 (MQ=255)
                             cAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTg                                      <  1:1484347/71‑1 (MQ=255)
                             cAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTg                                      <  1:1558808/71‑1 (MQ=255)
                                gTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTg                                      <  1:1888660/68‑1 (MQ=255)
                                gTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTGCAt                                   <  1:869091/71‑1 (MQ=255)
                                gTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCa                                                             <  1:725360/45‑1 (MQ=255)
                                  cGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTGCa                                    >  1:712127/1‑68 (MQ=255)
                                  cGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGc                                 >  1:2150665/1‑71 (MQ=255)
                                    ggCGAGTGTAATCAATTTCGCGGAAATCGACAGCTTTATCAGAAAGATggg                                                   >  1:404755/1‑51 (MQ=255)
                                    ggCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAg                                                            <  1:1848019/42‑1 (MQ=255)
                                    ggCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATggg                                                   >  1:1143610/1‑51 (MQ=255)
                                          tgtAATCAATTTCGCGGAAATCGACAGTGTTATCAGaaa                                                         <  1:508598/39‑1 (MQ=255)
                                          tgtAATCAATTTCGCGGAAATCGACAGTGTTATCAGaaa                                                         <  1:407858/39‑1 (MQ=255)
                                          tgtAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCt                                       <  1:1553388/57‑1 (MQ=255)
                                          tgtAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCt                                       <  1:1342974/57‑1 (MQ=255)
                                            tAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCttt                       >  1:417098/1‑71 (MQ=255)
                                            tAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCttt                       >  1:605846/1‑71 (MQ=255)
                                            tAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCtt                        <  1:1136973/70‑1 (MQ=255)
                                            tAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCtt                        <  1:499035/70‑1 (MQ=255)
                                              aTCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCttt                       >  1:1754517/1‑69 (MQ=255)
                                              aTCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCttt                       >  1:1188419/1‑69 (MQ=255)
                                              aTCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTga                     <  1:821362/71‑1 (MQ=255)
                                              aTCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTga                     <  1:1898883/71‑1 (MQ=255)
                                               tCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGc                                               <  1:2049904/44‑1 (MQ=255)
                                               tCAATTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGa                                           <  1:1335671/48‑1 (MQ=255)
                                               tCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCttt                       >  1:2120995/1‑68 (MQ=255)
                                                cAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCttt                       >  1:124272/1‑67 (MQ=255)
                                                cAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCttt                       >  1:1981479/1‑67 (MQ=255)
                                                 aaTTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCa                                             >  1:1669969/1‑44 (MQ=255)
                                                 aaTTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTg                                      <  1:891449/51‑1 (MQ=255)
                                                 aaTTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGAt                  <  1:638593/71‑1 (MQ=255)
                                                 aaTTTCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGAt                  >  1:2164258/1‑71 (MQ=255)
                                                 aaTTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGaa                                          >  1:1367643/1‑47 (MQ=255)
                                                 aaTTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGaa                                          >  1:2080870/1‑47 (MQ=255)
                                                     tCGCGGAAATCGACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGATGAg               >  1:245385/1‑70 (MQ=255)
                                                     tCGCGGAAATCGACAGCGTTATCAGAAAGATGGGt                                                  >  1:468153/1‑35 (MQ=255)
                                                     tCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGATGAGc              >  1:985399/1‑71 (MQ=255)
                                                     tCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCAAGAATCTGCATGCCCTGGCCTTTgaga                   >  1:782625/1‑66 (MQ=255)
                                                         ggAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTgag                    <  1:1370269/61‑1 (MQ=255)
                                                         ggAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTgag                    <  1:1043291/61‑1 (MQ=255)
                                                         ggAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTgag                    <  1:1030625/61‑1 (MQ=255)
                                                             aTCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGATGAGCGACGGc        <  1:82673/69‑1 (MQ=255)
                                                               cGACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGATGAGCGACGGCATCg    >  1:244802/1‑71 (MQ=255)
                                                               agACAGTGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGATGAg               >  1:758304/2‑60 (MQ=255)
                                                                gACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGATGAGCGACGGCATCGc   >  1:1039778/1‑71 (MQ=255)
                                                                 aCAGTGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGATGAGCGACGGCATCGcc  <  1:1676591/71‑1 (MQ=255)
                                                                  cAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGATGAGCGACGGCATCGcc  >  1:751368/1‑70 (MQ=255)
                                                                     |                                                                  
TGCCCGTTTTCTCCTGTCCCATCAAAATGCAGGTCGGGCGAGTGTAATCAATTTCGCGGAAATCGACAGCGTTATCAGAAAGATGGGTTGCCAGAATCTGCATGCCCTGGCCTTTGAGATGAGCGACGGCATCGCC  >  minE/2516587‑2516722

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