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 915,606 C→T 28.4% V52V (GTC→GTT)  ycjF → conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE915,6060CT28.4% 90.0 / 34.0 84V52V (GTC→GTT) ycjFconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (30/30);  new base T (4/20);  total (34/50)
Fisher's exact test for biased strand distribution p-value = 6.38e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAAAATCAGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGATGGGAGGGCT  >  minE/915541‑915674
                                                                 |                                                                    
gAAAATCAGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGa                                                                    <  1:1841183/68‑1 (MQ=255)
gAAAATCAGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGa                                                                    <  1:3240454/68‑1 (MQ=255)
   aaTCAGGCGCAAAATTTTGCCCCAGCCACGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCg                                                                >  1:713080/1‑69 (MQ=255)
   aaTCAGGCGCAAAATTTTGCCCCAGCCACGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCg                                                                >  1:472637/1‑69 (MQ=255)
   aaTCAGGCGCAAAATTTTGCCCCAGCCACGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCg                                                                >  1:3044757/1‑69 (MQ=255)
   aaTCAGGCGCAAAATTTTGCCCCAGCCACGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCg                                                                >  1:3369714/1‑69 (MQ=255)
     tCAGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGt                                                              <  1:977760/69‑1 (MQ=255)
     tCAGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGt                                                              <  1:1597176/69‑1 (MQ=255)
     tCAGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGt                                                              <  1:2221946/69‑1 (MQ=255)
     tCAGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGt                                                              <  1:2435398/69‑1 (MQ=255)
     tCAGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGt                                                              <  1:1125791/69‑1 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:3105065/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:37611/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:2980140/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:2709471/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:260296/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:649640/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:945360/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:1790034/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:172796/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:1046424/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTaa                                                            >  1:1444269/1‑69 (MQ=255)
       aGGCGCAAAATTTTGCCC‑‑‑CCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATgg                                                         >  1:1662482/1‑69 (MQ=255)
         gcgcAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCACGAAGAAGAGGGGCAAGTCGAAGCGGTAATg                                                          <  1:1793776/69‑1 (MQ=255)
                            ccACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGa                                       <  1:2567360/69‑1 (MQ=255)
                            ccACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGa                                       <  1:2441553/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGTTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:815063/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1011695/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:3426919/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1328745/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:2993510/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1480938/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:266895/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1504681/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1507664/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:964576/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:2237889/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1684446/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1913508/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1589825/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1758869/69‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGT‑ATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1559644/68‑1 (MQ=255)
                               cGCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGATGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1516707/69‑1 (MQ=255)
                                gCTCGATGAAGCGCAGGAAGAAGAGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:1133543/68‑1 (MQ=255)
                                      cgaAGCTCAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGcc                              <  1:2770059/68‑1 (MQ=255)
                                      cgaAGCGCATGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGGTACGTCCGAAACGCAGcc                              <  1:3217680/68‑1 (MQ=255)
                                      cgaAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGcc                              <  1:676010/68‑1 (MQ=255)
                                             cAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGCCGCAGCGTTACGTCCGAAACg                                   >  1:2165309/1‑56 (MQ=255)
                                             cAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGgcg                       >  1:598379/1‑68 (MQ=255)
                                             cAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGgcg                       >  1:72454/1‑68 (MQ=255)
                                             cAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGgcg                       >  1:168752/1‑68 (MQ=255)
                                             cAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGgcg                       >  1:1468547/1‑68 (MQ=255)
                                             cAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGgcg                       >  1:2705674/1‑68 (MQ=255)
                                             cAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGgcg                       >  1:1577676/1‑68 (MQ=255)
                                             cAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTT‑CGTCCGAAACGCAGCCTGTGgcgc                      >  1:2021488/1‑68 (MQ=255)
                                                    aagaGGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:645265/48‑1 (MQ=255)
                                                     agagGGGCAAGTTGAAGCGGTGATGGACGCAGCGTTACGTCCGAAAc                                    <  1:3377214/47‑1 (MQ=255)
                                                     agagGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:3080764/69‑1 (MQ=255)
                                                     agagGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:2069287/69‑1 (MQ=255)
                                                          ggCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTgg                         >  1:3430697/1‑53 (MQ=255)
                                                          ggCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCa                     >  1:1187723/1‑57 (MQ=255)
                                                          ggCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGAt           >  1:2074549/1‑67 (MQ=255)
                                                          ggCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGAt           >  1:2370837/1‑67 (MQ=255)
                                                          ggCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGAt           >  1:1674879/1‑67 (MQ=255)
                                                          ggCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGAt           >  1:2311082/1‑67 (MQ=255)
                                                          ggCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGAt           >  1:3000369/1‑67 (MQ=255)
                                                          ggCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGAt           >  1:2619855/1‑67 (MQ=255)
                                                          ggCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGAt           >  1:370872/1‑67 (MQ=255)
                                                          ggCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCC‑GTGGCGCAAAATGGTGATggg        >  1:2088961/1‑69 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:147750/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:109367/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:1131305/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:926405/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:1145204/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:373633/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:3380164/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:1196360/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:3220863/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:3154227/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:3079792/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:2287173/63‑1 (MQ=255)
                                                           gCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGt              <  1:2245020/63‑1 (MQ=255)
                                                             aaGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGATGGGAg      <  1:2580212/69‑1 (MQ=255)
                                                             aaGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGATGGGAg      <  1:1667582/69‑1 (MQ=255)
                                                                 cGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGATGGGAGggct  >  1:953434/1‑69 (MQ=255)
                                                                 |                                                                    
GAAAATCAGGCGCAAAATTTTGCCCCGGCCACGCTCGACGAAGCGCAGGAAGAAGAGGGGCAAGTCGAAGCGGTAATGGACGCAGCGTTACGTCCGAAACGCAGCCTGTGGCGCAAAATGGTGATGGGAGGGCT  >  minE/915541‑915674

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