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 F1 I0 R2 5 11.0 518987 97.1% 503936 64.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,359,876 C→T 42.9% noncoding (1219/2905 nt) rrlA ← 23S ribosomal RNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,359,8760CT42.9% 7.9 / 23.1 21noncoding (1219/2905 nt)rrlA23S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base C (10/2);  new base T (4/5);  total (14/7)
Fisher's exact test for biased strand distribution p-value = 1.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGC  >  minE/2359823‑2359935
                                                     |                                                           
aTCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTa                                            >  1:181091/1‑71 (MQ=34)
   gTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAg                                         <  1:179007/71‑1 (MQ=255)
      aCTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAAc                                      >  1:341756/1‑71 (MQ=34)
         tATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCt                                   >  1:70113/1‑71 (MQ=34)
          aTGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTc                                  >  1:147979/1‑71 (MQ=34)
          aTGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTc                                  >  1:355170/1‑71 (MQ=34)
          aTGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGc                                    <  1:217680/69‑1 (MQ=255)
          aTGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTc                                  >  1:296676/1‑71 (MQ=255)
          aTGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTc                                  >  1:155491/1‑71 (MQ=255)
             tCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTcccc                               <  1:431366/71‑1 (MQ=11)
             tCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTccc                                <  1:417954/70‑1 (MQ=255)
               aGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCt                              >  1:41886/1‑70 (MQ=35)
                  aTTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTAcc                           >  1:155361/1‑70 (MQ=255)
                      gCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTACCcaaca                      <  1:16949/71‑1 (MQ=255)
                           tCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTcccc                               >  1:106781/1‑57 (MQ=35)
                            cTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTAccc                          >  1:115077/1‑61 (MQ=35)
                            cTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTAc                            >  1:411074/1‑59 (MQ=35)
                                tACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAgtg            >  1:19492/1‑71 (MQ=255)
                                     ccAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAacaaca                   <  1:395830/59‑1 (MQ=38)
                                         cATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTAc                            >  1:215772/1‑46 (MQ=11)
                                          aTGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGc  <  1:31064/71‑1 (MQ=255)
                                                     |                                                           
ATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGC  >  minE/2359823‑2359935

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A