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
A5 F28 I3 R1 375 42.1 2927644 71.4% 2090337 57.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 2,866,110 T→A intergenic (‑20/+160) rpoS ← / ← nlpD RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,866,1100TA100.0% 99.2 / NA 31intergenic (‑20/+160)rpoS/nlpDRNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (31/0);  total (31/0)

GCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCT  >  W3110S.gb/2866059‑2866125
                                                   |               
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta        >  1:2311864/1‑61 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:1251522/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:9530/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:894712/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:760074/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:61140/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:544463/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:2896256/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:2892990/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:2844398/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:1391012/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:1558458/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:2068819/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:2006155/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa       >  1:2411576/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTCCCAATTCTACTaa       >  1:1661798/1‑62 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGCTTCCAATActacta        >  1:501089/1‑61 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCCCTGGGTTCCAATTCTACTAAGGCCt  >  1:2580693/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGcc   >  1:947148/1‑61 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:452462/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:1204480/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:1371529/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:610/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:594010/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:551156/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:2377571/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:2822481/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:2738086/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:2705047/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:2685251/1‑62 (MQ=255)
     cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt  >  1:2552750/1‑62 (MQ=255)
                                                   |               
GCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCT  >  W3110S.gb/2866059‑2866125

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