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 F2 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,715,428 |
T→G |
intergenic (+19/+260) |
BW25113_RS25300 → / ← glyS |
IS3‑like element IS150 family transposase/glycine‑‑tRNA ligase subunit beta |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,715,428 | 0 | T | G | 85.0%
| 50.7
/ 2.7
| 20 | intergenic (+19/+260) | BW25113_RS25300/glyS | IS3‑like element IS150 family transposase/glycine‑‑tRNA ligase subunit beta |
| Reads supporting (aligned to +/- strand): ref base T (2/1); new base G (9/8); total (11/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
ATTAGCCTGAAATTAAAAGGTCTGACTCCAATTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACA > NZ_CP009273/3715341‑3715501
|
aTTAGCCTGAAATTAAAAGGTCTGACTCCAATTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCa < 2:32011/90‑1 (MQ=255)
aTTAGCCTGAAATTAAAAGGTCTGACTCCAATTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCa > 2:120761/1‑90 (MQ=255)
aaaTTAAAAGGTCTGACTCCAATTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAAC‑TTTTGGGGGCAGTACAAACtt < 2:252229/90‑1 (MQ=255)
aaaGGTCTGACTCCAATTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGAtt < 2:58165/90‑1 (MQ=255)
aaaGGTCTGACTCCAATTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGAtt < 2:282520/90‑1 (MQ=255)
aaTTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGAtt > 2:396417/1‑76 (MQ=255)
aaTTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGAtt < 1:396417/76‑1 (MQ=255)
gACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCt > 1:164448/1‑90 (MQ=255)
tataTGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCg > 2:130312/1‑90 (MQ=255)
cTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATa < 1:209693/90‑1 (MQ=255)
tCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATAc > 1:196847/1‑90 (MQ=255)
gtgtTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCt > 1:284850/1‑90 (MQ=255)
tgtTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTg > 2:223286/1‑90 (MQ=255)
tGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAAc < 1:429320/90‑1 (MQ=255)
tGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAAc < 2:196847/90‑1 (MQ=255)
tGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAAc < 2:36990/90‑1 (MQ=255)
gTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACa > 1:390329/1‑90 (MQ=255)
gTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACa > 1:25125/1‑90 (MQ=255)
gTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACa > 1:91689/1‑90 (MQ=255)
gTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACa > 2:270578/1‑90 (MQ=255)
|
ATTAGCCTGAAATTAAAAGGTCTGACTCCAATTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACA > NZ_CP009273/3715341‑3715501
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AAAGGTCTGACTCCAATTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACAGTCTCAAGC > NZ_CP009273/3715356‑3715510
|
ACAGGTCTGACTCCAATTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGG < SRR3722113.400561/100‑1 (MQ=60)
ATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCT > SRR3722113.165789/1‑100 (MQ=60)
CCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATAC > SRR3722113.198377/1‑100 (MQ=60)
TATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCT > SRR3722113.287424/1‑100 (MQ=60)
CTCGTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAA < SRR3722113.211303/100‑1 (MQ=60)
GTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACA > SRR3722113.25338/1‑100 (MQ=60)
GTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACA > SRR3722113.394417/1‑100 (MQ=60)
GTGTTTAACTGTCCAACTTTTTGGGGGCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACA > SRR3722113.92518/1‑100 (MQ=60)
TGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACAGTCTCAAGC < SRR3722113.433863/100‑1 (MQ=60)
|
AAAGGTCTGACTCCAATTGAATATCGGAATCAGACCTATATGCCTCGTGTTTAACTGTCCAACTTTTTGGGGTCAGTACAAACTTTGATTTATAGTCAGGTGGGGCTTTTCTCTGTCTGCCTTTCGGTGAATACCTGAGACAAACAGTCTCAAGC > NZ_CP009273/3715356‑3715510
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
