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
A3 F53 I1 R1 62 81.2 3465250 98.6% 3416736 145.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947_CJ‑RC 3,845,705 +G intergenic (‑72/+26) PP_3394 ← / ← PP_3395 3‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC3,845,7031.G100.0% 78.8 / NA 23intergenic (‑70/+28)PP_3394/PP_33953‑hydroxy‑3‑methylglutaryl‑CoA lyase/LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (14/9);  total (14/9)

CTGTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑GGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGC  >  NC_002947_CJ‑RC/3845561‑3845816
                                                                                                                                               |                                                                                                                 
ctgTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑ggg                                                                                                                >  4:217597/1‑145 (MQ=255)
  gTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑gggctgg                                                                                                            <  4:73310/148‑6 (MQ=255)
   tCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑gggctga                                                                                                            <  1:170624/147‑6 (MQ=255)
    cGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGAta                                                                                                           >  8:189977/1‑147 (MQ=255)
         tGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCg                                                                                                      >  2:338404/1‑148 (MQ=255)
           aTCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTc                                                                                                    <  2:78193/148‑1 (MQ=255)
               cTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGcc                                                                                                <  4:204638/148‑1 (MQ=255)
                 tGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGGTACAACCTCAGcccc                                                                                              >  4:244972/1‑146 (MQ=255)
                   cAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGa                                                                                            <  1:338404/148‑1 (MQ=255)
                   cAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCAACGa                                                                                            >  6:196118/1‑148 (MQ=255)
                    aGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGAt                                                                                           <  5:296966/148‑1 (MQ=255)
                       ctctGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGa                                                                                        <  1:11589/148‑1 (MQ=255)
                           gCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAg                                                                                    >  8:184754/1‑148 (MQ=255)
                            cAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAg                                                                                    <  7:184754/147‑1 (MQ=255)
                             aaGCCATCGCGCAGGCCTACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTGGCTGACGATGGATCAGcc                                                                                  <  3:312941/148‑1 (MQ=38)
                             aaGCCATCGCGCAGGCCGACTTCATTGATTTTTATTGTTGTCATCGCGGTCTCTCTGTCTGATGCGTTGAGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCTGcc                                                                                  <  4:56173/148‑1 (MQ=255)
                               gCCTTCGGGCTGGCGGAGTGCATTGTTTGTTTTTGTTGTCATCGCGGTCTCTTTGTCTGTCGCGTTGCGCCTGATTATGAGCTGGATGACGGGCAGAATTGCCGTGTTTCGCGGGCTGTTCCTTCGTCTCCCACGATGGATCTGCCcg                                                                                <  8:440862/148‑1 (MQ=255)
                                    cgcgCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGAACCATCGTCACCCCCGAAGGATCAGCCCGCGccc                                                                           >  2:72100/1‑148 (MQ=255)
                                          ggCCGACTTCATAGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCAGAAACATACTCACCCACCAAGGAAAAGCCCCCGCCCAGcccc                                                                     >  7:135330/1‑146 (MQ=255)
                                            ccGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTTATCCATAGTCAGCCACGATGGATCAGCCACCGCCCTGCCATGc                                                                   >  6:302641/1‑148 (MQ=255)
                                                 ttCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCGGCCAGGCCGGTg                                                              >  8:112966/1‑148 (MQ=255)
                                                          tgttattgttGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTTATACATAGTCAGCCACGATGGATAAGCCCGCGCCCAGCCAGGCCGGTGCACgcagc                                                      >  8:296428/1‑147 (MQ=255)
                                                                  ttgtCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATACAAAGTCAGCCACCAAGGATCAGCCCGCGCCCTGCCAGGCCGGTTCCAGCAGCAACAcgtgg                                             >  8:222907/1‑148 (MQ=255)
                                                                                         gAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATACATGGTGAGCCACGGTTGATAAGCCCGCGCCCTGCCAGGTGGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAg                      >  7:119859/1‑148 (MQ=255)
                                                                                                         cTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCAGAAACAACGTCAGCCACGAAGGGTCAGCCCGCGCCCAGCCCGGGCGGGGGACCCAGCCACCGGTGGTGAAGCAGGCGCCCAGCCGGCCCCGAGAGCCGGTGcccg      >  8:86005/1‑146 (MQ=255)
                                                                                                             gagCTGGATGACGGGCAGAAAAGACGTGTTTCGCGGGCTGATAAAAAGTAAGCCACGAATGGTAAGCCCCCCCCCAGGCCGGCCGGGGGACCCAGCAACACGTGGTGAAGCAGGCGCCCAGCCGCCCGCGAGAGCGGGTGCCgggggc  >  2:330355/1‑144 (MQ=255)
                                                                                                                                               |                                                                                                                 
CTGTCGGCATGATCACTTGCAGGCTCTGCAAGCCATCGCGCAGGCCGACTTCATTGATTGTTATTGTTGTCATCGCGGTCTCTCTGTCTGAAGCGTTGCGCCAGACTAAGAGCTGGATGACGGGCAGAAAAGACGTGTTTCGC‑GGCTGATCCATCGTCAGCCACGATGGATCAGCCCGCGCCCTGCCAGGCCGGTGCACGCAGCAACAGGTGGTCAAGCAGGCGCCGAGCCGACAGCGAGAGCGTGTGCCGGTCGC  >  NC_002947_CJ‑RC/3845561‑3845816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A