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 F28 I3 R1 178 99.0 1887089 95.3% 1798395 63.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 2,879,292 A→T L138* (TTA→TAA)  ygcI ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,879,2920AT98.9% 325.2 / ‑4.1 87L138* (TTA→TAA) ygcIhypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (0/86);  total (0/87)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

GGTGTATACCGAGGCTTTAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACG  >  W3110S.gb/2879274‑2879354
                  |                                                              
ggTGTATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:416509/65‑1 (MQ=255)
 gtgtATAGCGAGGCTTTTATACTGCTTTTTCTAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1057112/64‑1 (MQ=39)
 gtgtATACCTAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1825518/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATTGGgtgt                  <  1:1206212/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:387806/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:5709/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:550128/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:52158/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:503089/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:472994/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:446005/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:43503/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:405406/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:400770/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:582029/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:370335/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:352690/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:349549/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:345251/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:282750/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:276282/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:26630/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:244768/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:752740/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:984249/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:923918/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:831441/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:820078/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:819977/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:804193/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:797447/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:791702/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:788724/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:767599/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:573663/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:75261/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:751996/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:72513/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:715624/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:714314/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:624155/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:616094/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:590665/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:190609/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1183886/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:241100/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1509111/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1508559/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1474730/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1342146/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1275091/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1270510/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1237764/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1206881/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1189426/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1515520/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1153082/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1148689/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1112676/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1111825/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1100036/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1095213/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1088878/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1084285/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1054901/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1708815/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1016586/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1869142/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1865063/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1861598/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1856675/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1854238/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1814988/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1783510/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1781088/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1526325/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1699941/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1659748/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1628793/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1623633/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:159232/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:158699/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1577254/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1541100/64‑1 (MQ=255)
 gtgtATACCGAGGCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgg                  <  1:911588/64‑2 (MQ=255)
            ggCTTTTATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGgtgt                  <  1:1288765/53‑1 (MQ=255)
                ttAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACg  <  1:519410/65‑1 (MQ=255)
                  |                                                              
GGTGTATACCGAGGCTTTAATACTGCTTTTTCAAGTTCTGAGATAACCATCGTTGCATGGGGTGTTAACCAGAGAGCGACG  >  W3110S.gb/2879274‑2879354

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A