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 F8 I0 R2 5 12.5 627370 96.8% 607294 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,359,876 C→T 31.8% noncoding (1219/2905 nt) rrlA ← 23S ribosomal RNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,359,8760CT31.8% 30.0 / 16.0 22noncoding (1219/2905 nt)rrlA23S ribosomal RNA
Reads supporting (aligned to +/- strand):  ref base C (7/8);  new base T (3/4);  total (10/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01

CCGCTTTATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCT  >  minE/2359816‑2359939
                                                            |                                                               
ccGCTTTATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTca                                                        >  1:576173/1‑70 (MQ=255)
 cGCTTTATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTca                                                        >  1:409476/1‑69 (MQ=31)
  gCTTTATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAg                                                     >  1:97746/1‑71 (MQ=255)
      tATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGc                                                   <  1:514593/69‑1 (MQ=35)
       aTCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTa                                                >  1:87924/1‑71 (MQ=34)
        tCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTa                                                <  1:289413/70‑1 (MQ=255)
                 aTGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTc                                      >  1:394124/1‑71 (MQ=34)
                  tGTCAGCATTCGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTc                                      <  1:109682/70‑1 (MQ=255)
                        cATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTAc                                <  1:20969/70‑1 (MQ=35)
                            cGCACTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGaa                                           >  1:620040/1‑55 (MQ=11)
                              cACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTa                                                <  1:250971/48‑1 (MQ=38)
                                cTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAacaaca                       <  1:377781/71‑1 (MQ=35)
                                cTTCTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCt                                                  <  1:318212/44‑1 (MQ=11)
                                  tCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCca                             <  1:482831/63‑1 (MQ=35)
                                   cTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAAcaca                     >  1:16920/1‑70 (MQ=40)
                                   cTGATACCTCCAGCATACCTCACAGTACACCTTCACAGGCTTACAGAACGCTCCCCTACCCaacaacgc                      <  1:65253/69‑3 (MQ=11)
                                        aCCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAgtgt               >  1:49206/1‑71 (MQ=255)
                                           tCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAacac                      >  1:368486/1‑61 (MQ=39)
                                             cAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCt           <  1:547301/70‑1 (MQ=255)
                                                cATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCg       >  1:105782/1‑71 (MQ=255)
                                                    ccTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGc   <  1:528251/71‑1 (MQ=255)
                                                     cTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCt  <  1:220123/71‑1 (MQ=255)
                                                            cacaCCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAgt                 >  1:371697/1‑49 (MQ=255)
                                                            |                                                               
CCGCTTTATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCACAGGCTTACAGAACGCTCCCCTACCCAACAACACATAGTGTCGCTGCCGCAGCT  >  minE/2359816‑2359939

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