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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,924,650 C→T 30.0% H339Y (CAT→TAT)  galR → DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,924,6500CT30.0% 90.0 / 44.7 60H339Y (CAT→TAT) galRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (26/16);  new base T (6/12);  total (32/28)
Fisher's exact test for biased strand distribution p-value = 5.24e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAATTCTTCGATGGTCTGGC  >  minE/1924581‑1924714
                                                                     |                                                                
aCTAATGTCTTTAGTCCCACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcatca                                                                 >  1:2645540/1‑71 (MQ=255)
   aaTGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcatca                                                                 >  1:2317958/1‑68 (MQ=255)
       tCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAAc                                                           >  1:3501747/1‑70 (MQ=255)
        cTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAAc                                                           >  1:992267/1‑69 (MQ=255)
           tAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTcatcat                                                                >  1:92828/1‑61 (MQ=255)
           tAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGc                                                       <  1:2812026/70‑1 (MQ=255)
           tAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGc                                                       <  1:334661/70‑1 (MQ=255)
                cGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTaa                                                 >  1:583103/1‑71 (MQ=255)
                cGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTa                                                  <  1:3403271/70‑1 (MQ=255)
                  aCGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAAcc                                               >  1:1072089/1‑71 (MQ=255)
                    gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCg                                              >  1:1300586/1‑70 (MQ=255)
                    gCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCg                                              >  1:2598927/1‑70 (MQ=255)
                     cTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCg                                              >  1:3805644/1‑69 (MQ=255)
                       ggTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGa                                                     <  1:2779318/60‑1 (MQ=255)
                       ggTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGt                                          >  1:3944099/1‑71 (MQ=255)
                       ggTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGt                                          >  1:2723467/1‑71 (MQ=255)
                        gTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGt                                          >  1:3740671/1‑70 (MQ=255)
                        gTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGt                                          >  1:265050/1‑70 (MQ=255)
                          aCGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTa                                        >  1:2382274/1‑70 (MQ=255)
                             tcgtcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGc                                    <  1:1521330/71‑1 (MQ=255)
                             tcgtcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGc                                    <  1:3104918/71‑1 (MQ=255)
                              cgtcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGc                                    <  1:2123388/70‑1 (MQ=255)
                               gtcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCaa                                  >  1:703120/1‑71 (MQ=255)
                                tcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATTATGCAACCAGc                                                       <  1:1531850/49‑1 (MQ=255)
                                tcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATTATGCAACCAGc                                                       <  1:1536798/49‑1 (MQ=255)
                                tcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCa                                                         >  1:3928687/1‑47 (MQ=255)
                                tcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAAt                                 <  1:1793073/71‑1 (MQ=255)
                                tcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAAt                                 <  1:860886/71‑1 (MQ=255)
                                tcATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAAt                                 <  1:2785948/71‑1 (MQ=255)
                                 cATTCAGTGTCAACTCCGTCGCTGGAGGCAAGtcatca                                                                 >  1:411289/1‑38 (MQ=255)
                                 cATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTaa                                                 >  1:3624435/1‑54 (MQ=255)
                                  aTTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGCAAtt                                <  1:1536827/70‑1 (MQ=255)
                                   ttCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATTATGCa                                                             <  1:2057074/40‑1 (MQ=255)
                                   ttCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATTATGCa                                                             <  1:3173563/40‑1 (MQ=255)
                                   ttCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGCAAtt                                <  1:474253/69‑1 (MQ=255)
                                    tCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGc                                    <  1:1988416/64‑1 (MQ=255)
                                     cAGTGTCAACTCCGTCGCTGGAGGCAAGTCATTATGCAAcc                                                          >  1:3485428/1‑41 (MQ=255)
                                        tgtCAACTCCGTCGCTGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGCAAt                                 >  1:2796504/1‑63 (MQ=255)
                                          tCAACTCCGTCGCTGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAgcgc                         >  1:1467553/1‑69 (MQ=255)
                                            aaCTCCGTCGCTGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGt                     <  1:899326/71‑1 (MQ=255)
                                            aaCTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAg                      >  1:1608053/1‑70 (MQ=255)
                                            aaCTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAg                      >  1:2428639/1‑70 (MQ=255)
                                              cTCCGTCGCTGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTaa                   >  1:3880113/1‑71 (MQ=255)
                                              cTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTaa                   >  1:331217/1‑71 (MQ=255)
                                                ccGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAtt                 >  1:3160358/1‑71 (MQ=255)
                                                ccGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAt                  >  1:3541615/1‑70 (MQ=255)
                                                ccGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAt                  >  1:505473/1‑70 (MQ=255)
                                                 cGTCGCTGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAttc                >  1:2480538/1‑71 (MQ=255)
                                                 cGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAtt                 <  1:1451094/70‑1 (MQ=255)
                                                  gTCGCTGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAttct               <  1:114077/71‑1 (MQ=255)
                                                  gTCGCTGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAttct               <  1:1050289/71‑1 (MQ=255)
                                                   tCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTaa                   >  1:3840658/1‑66 (MQ=255)
                                                     gCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAttcttc             >  1:1466364/1‑70 (MQ=255)
                                                     gCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAttcttc             <  1:604473/70‑1 (MQ=255)
                                                     gCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAttcttc             <  1:3505627/70‑1 (MQ=255)
                                                       tGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGc                                    <  1:522733/45‑1 (MQ=255)
                                                       tGGAGGCAAGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGc                                    <  1:3709634/45‑1 (MQ=255)
                                                       tGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAATTCTTCGAt          >  1:2472574/1‑71 (MQ=255)
                                                       tGGAGGCAAGTAATTATGCAACCAGCGACTAACCGCAGTTAAAGc                                    <  1:695887/45‑1 (MQ=255)
                                                         gAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAATTCTTCGATgg        >  1:2215776/1‑71 (MQ=255)
                                                          aGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAATTCTTCGATGGt       <  1:2967739/71‑1 (MQ=255)
                                                              aaGTCATTATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAATTCTTCGATGGTCTgg   >  1:1164843/1‑71 (MQ=255)
                                                               aGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAATTCTTCGATGGTCTGGc  <  1:909052/71‑1 (MQ=255)
                                                                gTCATCATGAAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAATTCTTCGATGGTCTGGc  >  1:31445/1‑70 (MQ=255)
                                                                 tcatcaTGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAAttcttc             <  1:1760563/58‑1 (MQ=255)
                                                                  catcatGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAATTCTTCGa           >  1:271852/1‑59 (MQ=255)
                                                                     catGCAACCAGCGACTAACCGCAGTTAAAGCAATTc                               >  1:2258137/1‑36 (MQ=255)
                                                                     |                                                                
ACTAATGTCTTTAGTCCGACGCTGGTACGTCGTCATTCAGTGTCAACTCCGTCGCTGGAGGCAAGTCATCATGCAACCAGCGACTAACCGCAGTTAAAGCAATTCCAGCGCCAGTAATTCTTCGATGGTCTGGC  >  minE/1924581‑1924714

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