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 2,371,447 A→G 48.6% F214L (TTT→CTT)  fre ← flavin reductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,371,4470AG48.6% ‑4.7 / 51.1 35F214L (TTT→CTT) freflavin reductase
Reads supporting (aligned to +/- strand):  ref base A (10/8);  new base G (12/5);  total (22/13)
Fisher's exact test for biased strand distribution p-value = 4.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.06e-01

TTATATCTCAGATAAATGCAAACGCATCGCCAAACAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGATATCATGCTCTGCCAGCGT  >  minE/2371378‑2371513
                                                                     |                                                                  
ttATATCTCAGATAAATGCAAACGCATCGCCAAACAGGCGATCTTCCCGCGCATTACGCTCACTGCaaaa                                                                    <  1:840425/70‑1 (MQ=255)
ttATATCTCAGATAAATGCAAACGCATCGCCAAACAGGCGATCTTCCCGCGCATTACGCTCACTGCaaaa                                                                    <  1:402383/70‑1 (MQ=255)
             aaaTGCAAACGCATCGCCAAACAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAGCAGATCGCGGTCaa                                                      >  1:1876180/1‑71 (MQ=255)
              aaTGCAAACGCATCGCCAAACAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAGCAGAt                                                               >  1:1600989/1‑61 (MQ=255)
              aaTGCAAACGCATCGCCAAACAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAGCAGATCGCGGGCaa                                                      <  1:89021/70‑1 (MQ=255)
                      cGCATCGCCAAACAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAACAGATcgc                                                            >  1:1709547/1‑56 (MQ=255)
                            gCCAAACAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCa                                        <  1:921216/70‑1 (MQ=255)
                            gCCAAACAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCa                                        >  1:1400406/1‑70 (MQ=255)
                                aaCAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAGCa                                                                  <  1:1045748/40‑1 (MQ=255)
                                aaCAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCAATCTCAAAACg                                   <  1:1390072/71‑1 (MQ=255)
                                 aCAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGt                                  >  1:1159776/1‑71 (MQ=255)
                                  cAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTc                                 <  1:1817885/71‑1 (MQ=255)
                                          cTTCCCGCGCATTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAAc                                    >  1:2173836/1‑60 (MQ=255)
                                           ttCCCGCGCATTACGCTCACTGCAAAGCAGATCGCGGGCAATTTTCGCCATCTCAAAAc                                    >  1:2113936/1‑59 (MQ=255)
                                           ttCCCGCGCATTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCaa                                       <  1:742400/56‑1 (MQ=255)
                                             cccGCGCATTACGCTCACTGCAAAGCAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCaa                           >  1:666105/1‑66 (MQ=255)
                                             cccGCGCATTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCaa                           <  1:2028684/66‑1 (MQ=255)
                                                    aTTACGCTCACTGCAAAGCAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGat                    <  1:437924/66‑1 (MQ=255)
                                                    aTTACGCTCACTGCAAAGCAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGat                    <  1:1228545/66‑1 (MQ=255)
                                                    aTTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGATATCAt               >  1:798897/1‑71 (MQ=255)
                                                     ttACGCTCACTGCAAAGCAGATCGCGGGCAATTTTCGCCATTTCAAAACGTCCGGCAAtata                       <  1:46472/62‑1 (MQ=255)
                                                       aCGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGa                     >  1:1773079/1‑62 (MQ=255)
                                                       aCGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGa                     >  1:1157345/1‑62 (MQ=255)
                                                       aCGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGa                     >  1:764244/1‑62 (MQ=255)
                                                       aCGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGa                     >  1:141185/1‑62 (MQ=255)
                                                         gCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGATATCATGctct          <  1:462353/71‑1 (MQ=255)
                                                         gCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGATATCATGctct          <  1:1061265/71‑1 (MQ=255)
                                                             aCTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGATATCATGCTCTGc        >  1:450345/1‑69 (MQ=255)
                                                                 cAAAGCAGATCGCGGGCAATTTTCGCCATCTCaaaa                                     >  1:850635/1‑36 (MQ=255)
                                                                 cAAAGCAGATCGCGGGCAATTTTCGCCATCTCaaaa                                     >  1:1704019/1‑36 (MQ=255)
                                                                 cAAAGCAGATCGCGGGCAATTTTCGCCATCTCaaaa                                     >  1:410261/1‑36 (MQ=255)
                                                                 cAAAGCAGATCGCGGGCAATTTTCGCCATCTCaaaa                                     >  1:199482/1‑36 (MQ=255)
                                                                 cAAAGCAGATCGCGGGCAATTTTCGCCATCTCaaaa                                     >  1:1685523/1‑36 (MQ=255)
                                                                 cAAAGCAGATCGCGGGCAATTTTCGCCATCTCAAAACGTc                                 >  1:39075/1‑40 (MQ=255)
                                                                 cAAAGCAGATCGCGGGCAATTTTCGCCATCTCAAAACGTc                                 >  1:1267612/1‑40 (MQ=255)
                                                                 cAAAGCAGATCGCGGGCAATTTTCGCCATCTCAAAACGTc                                 >  1:1378595/1‑40 (MQ=255)
                                                                 cAAAACAGATCGCGGGCAATTTTCTCCATCTCAAAACGTCCGGCAATATAGATATCATGCTCTGCCAGCGt  <  1:1255640/71‑1 (MQ=255)
                                                                   aaaCAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAg                      <  1:1501982/49‑1 (MQ=255)
                                                                   aaaCAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAg                      <  1:1847823/49‑1 (MQ=255)
                                                                     |                                                                  
TTATATCTCAGATAAATGCAAACGCATCGCCAAACAGGCGATCTTCCCGCGCATTACGCTCACTGCAAAACAGATCGCGGGCAATTTTCGCCATCTCAAAACGTCCGGCAATATAGATATCATGCTCTGCCAGCGT  >  minE/2371378‑2371513

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