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 1,598,488 C→T 32.6% A60A (GCG→GCA)  yfeT ← predicted DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,598,4880CT32.6% 61.5 / 40.5 49A60A (GCG→GCA) yfeTpredicted DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (21/12);  new base T (7/9);  total (28/21)
Fisher's exact test for biased strand distribution p-value = 2.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

TTCGTTTTCTCCCGGCTGGCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTGCCGT  >  minE/1598423‑1598557
                                                                 |                                                                     
ttCGTTTTCTCCCGGCTGGCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGcc                                                                  <  1:54965/71‑1 (MQ=255)
ttCGTTTTCTCCCGGCTGGAACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGcc                                                                  >  1:652318/1‑71 (MQ=255)
  cGTTTTCTCCCGGCTGGCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGcc                                                                  >  1:644136/1‑69 (MQ=255)
  cGTTTTCTCCCGGCTGGCACTGTATTCGCCTATTAACGCAATACGCAATTCAGTAAATCCTTGCGCGcc                                                                  >  1:242693/1‑69 (MQ=255)
   gTTTTCTCCCGGCTGGCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAg                                                               >  1:1667053/1‑71 (MQ=255)
   gTTTTCTCCCGGCTGGCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAg                                                               >  1:387372/1‑71 (MQ=255)
    ttttCTCCCGGCTGGCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCg                                                                 <  1:2035217/68‑1 (MQ=255)
      ttCTCCCGGCTGGCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGtt                                                             <  1:1661511/70‑1 (MQ=255)
        ctcCCGGCTGGCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGtttt                                                           <  1:1323244/70‑1 (MQ=255)
             ggCTGGCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCa                                                     <  1:400285/71‑1 (MQ=255)
                       gTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGa                                                                >  1:594534/1‑50 (MQ=255)
                        tATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGttttt                                                          <  1:857041/55‑1 (MQ=255)
                        tATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTAt                                          >  1:808280/1‑71 (MQ=255)
                          ttCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGc                                        >  1:1594205/1‑71 (MQ=255)
                            cGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTggg                                                       >  1:1298062/1‑54 (MQ=255)
                             gCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTc                                      <  1:1031940/70‑1 (MQ=255)
                             gCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCg                                     <  1:1527550/71‑1 (MQ=255)
                             gCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCg                                     <  1:1202408/71‑1 (MQ=255)
                                  ttAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCAc                                             <  1:575947/58‑1 (MQ=255)
                                    aaCGCCATACGCAATTCATTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATg                                         >  1:318937/1‑60 (MQ=255)
                                    aaCGCCATACGCAATTCAGTAAATCCTTGTGCGACGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGc                               >  1:260195/1‑70 (MQ=255)
                                     aCGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCt                              <  1:279217/70‑1 (MQ=255)
                                     aCGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCt                              >  1:1488694/1‑70 (MQ=255)
                                     aCGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCt                              >  1:1528322/1‑70 (MQ=255)
                                     aCGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCt                              >  1:340674/1‑70 (MQ=255)
                                       gCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCt                              <  1:1742297/68‑1 (MQ=255)
                                          aTACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGcc                        <  1:1029936/71‑1 (MQ=255)
                                           tACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCAc                                             <  1:387358/49‑1 (MQ=255)
                                            aCGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGcc                        >  1:1637192/1‑69 (MQ=255)
                                             cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAAt                                                  >  1:1329833/1‑42 (MQ=255)
                                             cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCa                                              >  1:2056528/1‑46 (MQ=255)
                                             cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCa                                              >  1:1896349/1‑46 (MQ=255)
                                             cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCa                                              >  1:1551716/1‑46 (MQ=255)
                                             cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGa                                    >  1:949247/1‑56 (MQ=255)
                                                aaTTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTg                  <  1:2035718/71‑1 (MQ=255)
                                                aaTTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTg                  >  1:265017/1‑71 (MQ=255)
                                                aaTTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCAGAGCTg                  >  1:1290510/1‑71 (MQ=255)
                                                 aTTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCa                                              <  1:842495/42‑1 (MQ=255)
                                                   tCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACt                                            >  1:1000409/1‑42 (MQ=255)
                                                    cAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGc                                        <  1:383022/45‑1 (MQ=255)
                                                    cAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGc                                        <  1:771954/45‑1 (MQ=255)
                                                     aGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGAc                                   >  1:2205870/1‑49 (MQ=255)
                                                       tAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc            >  1:412993/1‑70 (MQ=255)
                                                         aaTCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCAt         >  1:125185/1‑71 (MQ=255)
                                                         aaTCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCAt         >  1:1656908/1‑71 (MQ=255)
                                                         aaTCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTAt                                          >  1:1548719/1‑38 (MQ=255)
                                                         aaTCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGtt                <  1:428449/64‑1 (MQ=255)
                                                         aaTCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGtt                <  1:1787549/64‑1 (MQ=255)
                                                             cTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTGc     <  1:1104780/71‑1 (MQ=255)
                                                                gcgcgcCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTGcc    <  1:1483789/69‑1 (MQ=255)
                                                                 cgcgcCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTGCCGt  <  1:1205891/70‑1 (MQ=255)
                                                                 |                                                                     
TTCGTTTTCTCCCGGCTGGCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTGCCGT  >  minE/1598423‑1598557

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A