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 F56 I1 R1
|
11 |
18.4 |
473212 |
93.6% |
442926 |
129.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,279,705 |
G→A |
A943V (GCA→GTA) |
ebh_3 ← |
Extracellular matrix‑binding protein ebh |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,279,705 | 0 | G | A | 97.0%
| 75.8
/ NA
| 33 | A943V (GCA→GTA) | ebh_3 | Extracellular matrix‑binding protein ebh |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (15/17); minor base C (1/0); total (16/17) |
| Fisher's exact test for biased strand distribution p-value = 4.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAT > USA300TCH1516_ALE/2279580‑2279828
|
taGTCGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGTCTGTTTGTTTATGCATTTACTCTAGAATTGTTATTAGGTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACtg < 1:154535/129‑1 (MQ=255)
aGTTGATTCTACTTCTGGGTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAAAATTGTTATTAGCTTGCGGTTTAGCATTAGCATCCTCAGTTGCTGATGTTACtgt > 2:3906/1‑129 (MQ=255)
aGTTGATTCTACTTCTGGATTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTCCtgt > 2:33080/1‑129 (MQ=255)
ttGATTCTACTTCTGGTTTTCTAGTTATAGCGGTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGTATTGTTATTAGCTTGCGGTTTATCATTTGTATCATCAGTTGCTGATGTTACtgttg < 2:128935/129‑1 (MQ=255)
tCTACTTCTGGATTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATAATCAGATGCTGATATTACTGTTGTTTCa > 2:65284/1‑129 (MQ=255)
ttCTGGTGTGCTTGTTACGTCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACATTAGAATTGTTATTAGCTTGCGGTTTATCAGGGGGTGCATTAGTTGCTGTTGTTACTGGTGTTTCACCTGt < 2:95643/129‑1 (MQ=255)
cTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTATTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTGATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTg > 1:20022/1‑129 (MQ=255)
ggTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGca > 1:231973/1‑128 (MQ=255)
tttACTAGTTACATCGTTATCCATTGTCGTACTGTTTGTTGATGCATCTATACTTCAGGTGTTGTTGTCTTGCGGTTTTTCATTTGCATCATCAGTTGCTGAGGTTACTGTTGTTTCACCTGTTGCCGc < 1:109687/129‑1 (MQ=255)
aCATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTAGACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACTTGTTTCCGCATCACtatta > 2:195461/1‑129 (MQ=255)
tgcATTGTCGGGCTGTTTGTTGATGAATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGtgtt < 2:212250/127‑1 (MQ=255)
tCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTCTTTGGtgtt > 2:102971/1‑129 (MQ=255)
aTTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGTGGTTTATCTTTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTc < 1:96781/129‑1 (MQ=255)
tCGGACTGTTCGCTCATACAAATTCACTAGAATGGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGgag > 2:193378/1‑129 (MQ=255)
cgtttgttGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCCTTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGt > 2:219640/2‑129 (MQ=255)
gtttgttGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTATATCAATTGCAACATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTc > 1:58518/1‑129 (MQ=255)
ttgATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCCCTATTCTTTGGTGTTGTCGGAGAAGCGTCTGCtt > 2:159286/1‑129 (MQ=255)
atttACACTAGATTTTTGATTAGCTTGCGGTTTATCATTTTCATCTTCAGTTGCTGATGTTACTTTTGTTTCACCTGTTGCCGCATCACTATTATTTGTTGTTGTCGGAGAAGCGTCTGCTTTGCCAtt < 2:124854/126‑1 (MQ=255)
aTCTACACTAGATTTGTTTTTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCAtt < 2:32326/129‑1 (MQ=255)
gaGAATGGTTAGTAGCGTGCGGTTTATCGTTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCTATTAGCTgtcg < 2:98206/128‑1 (MQ=255)
gTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACTTGTTGCCGCATCAGTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGa < 1:197356/129‑1 (MQ=255)
tttttaGCTTTCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGTTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGAt < 2:40325/126‑1 (MQ=255)
attaGCTTGCGGTTTATTCTTTGCATCATCCGTTGCTGATGTTACTGTTGTTTCATCTGTTGCCGTTTCTTTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATAc < 1:225139/129‑1 (MQ=255)
gCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTa > 2:213533/1‑129 (MQ=255)
gCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTa > 2:163422/1‑129 (MQ=255)
cGGTTTATGCTTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGCTGTTGTCGGAGAAGCGTCTGTTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTg < 2:198275/129‑1 (MQ=255)
cGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTTTTTTGTTTTGTCGGTGAAGCGTCTGCTTGGCGATTAGCTGTCGTCTCAGATACGTTAGGTTg < 1:71015/129‑1 (MQ=255)
gttgtattatATGCAGCATCCGGTGCTGATGTGATTGTTGTTTCACCTCTTTCCGCAGCACTATTATTTGTTGTTTTCGGAGAAGCGTCTGCTTTGTCATTAGCTGTCGTCTCAGATTCGTTAGGTTGt < 2:195521/125‑1 (MQ=255)
tCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTa < 2:20022/129‑1 (MQ=255)
cATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTCCCATTAGCCGTCGTCTCCTCAACGTTAGGTTGTCCAGttt > 2:42397/1‑127 (MQ=255)
caGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTAGTATTGTCGGAGAAACGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTg > 1:23786/1‑129 (MQ=255)
aGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTAAGGGTGTCCAGTATTTTCTGGTGTTGc > 2:125296/1‑129 (MQ=255)
aTGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAt < 2:231973/129‑1 (MQ=255)
|
TAGTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAT > USA300TCH1516_ALE/2279580‑2279828
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
