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
A1 F17 I0 R2 276 45.3 3729697 93.0% 3468618 60.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,910,539 C→A 76.2% R590L (CGC→CTC)  relA ← (p)ppGpp synthetase I/GTP pyrophosphokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,910,5390CA76.2% 20.9 / 13.3 21R590L (CGC→CTC) relA(p)ppGpp synthetase I/GTP pyrophosphokinase
Reads supporting (aligned to +/- strand):  ref base C (2/3);  new base A (4/12);  total (6/15)
Fisher's exact test for biased strand distribution p-value = 5.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCGCGATGTGGTGCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGCGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTC  >  W3110S.gb/2910476‑2910591
                                                               |                                                    
cgcgcgATGTGGTGCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGttt                                                 <  1:3517137/69‑1 (MQ=255)
    cgATGTGGTGCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGCGGTTTTgcg                                             <  1:2795228/69‑1 (MQ=255)
    cgATGTGGTGCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGCGGTTTTgcg                                             <  1:2172507/69‑1 (MQ=255)
           gtgCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCgtg                                        >  1:2110231/1‑67 (MQ=255)
                tCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCttt                                 <  1:1714825/69‑1 (MQ=255)
                tCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCtt                                  <  1:123509/68‑1 (MQ=255)
                tCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCtt                                  <  1:2401343/68‑1 (MQ=255)
                         cAACACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGa                         <  1:1611408/68‑1 (MQ=255)
                          aaCACCTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTTCGGCGTGTAGCTTTTTTGCTGaa                        <  1:1107627/68‑1 (MQ=255)
                             acCTTCGACTACCACGCGACCGTTATCTTTACTGCGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTg                    >  1:3005959/1‑69 (MQ=255)
                               cTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCt                  <  1:2233137/69‑1 (MQ=255)
                               cTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCt                  <  1:1351593/69‑1 (MQ=255)
                               cTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCt                  <  1:1331832/69‑1 (MQ=255)
                               cTTCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCt                  <  1:695540/69‑1 (MQ=255)
                                ttCGACTACCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCttt                                 <  1:2395220/53‑1 (MQ=255)
                                       aCCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCtt                                  >  1:3083909/1‑45 (MQ=255)
                                       aCCACGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCGTTTTTGCTGAAGTTGCTTCAgcgc           >  1:2600780/1‑68 (MQ=255)
                                          aCGCGACCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCgcggcg       >  1:3392295/1‑69 (MQ=255)
                                               aCCGTTATCTTTACTGAGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTc  <  1:2592642/69‑1 (MQ=255)
                                                     aTCTTTACTGCGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTc                >  1:2813296/1‑49 (MQ=255)
                                                        tttACTGCGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAg              <  1:831459/48‑1 (MQ=255)
                                                               |                                                    
CGCGCGATGTGGTGCATCAGGTTGCCAACACCTTCGACTACCACGCGACCGTTATCTTTACTGCGGTTTTGCGGCGTGTAGCTTTTTTGCTGAAGTTGCTTCAGCGCGGCGGCGTC  >  W3110S.gb/2910476‑2910591

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A