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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
RA |
NZ_CP009273 |
1,659,576 |
T→C |
F14S (TTC→TCC) |
clcB → |
voltage‑gated ClC‑type chloride channel ClcB |
|
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
* | NZ_CP009273 | 1,659,576 | 0 | T | C | 95.2%
| 61.9
/ ‑3.8
| 21 | F14S (TTC→TCC) | clcB | voltage‑gated ClC‑type chloride channel ClcB |
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (15/5); total (15/6) |
Fisher's exact test for biased strand distribution p-value = 2.86e-01 |
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTTCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAG > NZ_CP009273/1659490‑1659661
|
ttttGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTTCCa < 2:790529/90‑1 (MQ=255)
gCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAAc < 1:321263/90‑1 (MQ=255)
tttCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTcgcg < 1:897748/90‑1 (MQ=255)
tttCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTcgcg > 2:531832/1‑90 (MQ=255)
gCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTc > 1:60786/1‑53 (MQ=255)
gCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTc < 2:60786/53‑1 (MQ=255)
gCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCtt > 2:189273/1‑90 (MQ=255)
tGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTttgccg > 1:830030/1‑90 (MQ=255)
tGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTttgccg > 2:332016/1‑90 (MQ=255)
catcTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTcgc < 1:926989/74‑1 (MQ=255)
catcTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTcgc > 2:926989/1‑74 (MQ=255)
catcTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTttgccgttgcc > 2:771475/1‑90 (MQ=255)
aTCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATg > 1:164776/1‑90 (MQ=255)
cGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGa < 2:422403/90‑1 (MQ=255)
gcgcACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATgctgct > 2:968539/1‑90 (MQ=255)
gcgcACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATgctgct > 2:500092/1‑90 (MQ=255)
gcgcACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATgctgct > 2:456362/1‑90 (MQ=255)
gcgcACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATgctgct > 2:382933/1‑90 (MQ=255)
cTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTgg > 2:12073/1‑90 (MQ=255)
cTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTgg > 1:94894/1‑90 (MQ=255)
aTGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAg > 1:265720/1‑90 (MQ=255)
|
TTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTTCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAG > NZ_CP009273/1659490‑1659661
|
Alignment Legend |
---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGGCTGGCCTCTTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTTCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAGTGGTTGTTCCTC > NZ_CP009273/1659479‑1659673
|
CGGCTGGCCTCTTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCC < SRR3722236.971582/100‑1 (MQ=60)
TGGCCTCTTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCG < SRR3722236.566621/100‑1 (MQ=60)
GCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGT < SRR3722236.325859/100‑1 (MQ=60)
GCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCctgtctcttatacacatctgacgctgc > SRR3722236.61640/1‑73 (MQ=60)
agacagGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCC < SRR3722236.943359/94‑1 (MQ=60)
TTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCG > SRR3722236.844510/1‑100 (MQ=60)
TTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCG < SRR3722236.913565/100‑1 (MQ=60)
ttcgtcggcagcgtcagatgtgtataagagacagCTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGT < SRR3722236.946933/66‑1 (MQ=60)
TCTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTctgtctcttatacacatctgacgctgccgacgaaggcttaggtgtagatctcggt > SRR3722236.775109/1‑45 (MQ=60)
CTACACATCTATCCGGATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATG > SRR3722236.167196/1‑100 (MQ=60)
GATCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGG > SRR3722236.96217/1‑100 (MQ=60)
TCTGCGCACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAG > SRR3722236.269608/1‑100 (MQ=60)
CACTATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAGTGGTTG > SRR3722236.787539/1‑100 (MQ=60)
ATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCtgtctcttatacacatctgacgctgccgac > SRR3722236.439234/1‑70 (MQ=60)
ATGTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTctgtctcttataca > SRR3722236.412555/1‑86 (MQ=60)
GTCCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAGTGGTTGTTCCTC > SRR3722236.713522/1‑100 (MQ=60)
|
CGGCTGGCCTCTTTTGCCGCAAAATAGTCGCCCGTGTTTCATTGCCCATTTCTGCTCATGCATCATCTACACATCTATCCGGATCTGCGCACTATGTTCCACCGTCTGCTTATCGCAACAGTCGTCGGTATTCTCGCGGCCTTTGCCGTTGCCGGGTTTCGTCATGCGATGCTGCTACTGGAGTGGTTGTTCCTC > NZ_CP009273/1659479‑1659673
|
Alignment Legend |
---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |