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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,584,892 |
G→A |
100% |
G124G (GGG→GGA) |
cysZ → |
predicted inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,584,892 | 0 | G | A | 75.9%
| 35.7
/ 8.0
| 33 | G124G (GGG→GGA) | cysZ | predicted inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (1/7); new base A (25/0); total (26/7) |
| Fisher's exact test for biased strand distribution p-value = 1.87e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CCGTTTAACGGTTTATTGGCTGAACAACTGGAAGCACGATTGACTGGCGCTACACCGCCAGATACCGGGATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGAAACGCG > minE/1584824‑1584935
|
ccGTTTAACGGTTTATTGGCTGAACAACTGGAAGCACGATTGACTGGCGCTACACCGCCAGATACCggg > 1:946742/1‑69 (MQ=255)
ccGTTTAACGGTTTATTGGCTGAACAACTGGAAGCACGATTGACTGGCGCTACACCGCCAGATACCggg > 1:909072/1‑69 (MQ=255)
ccGTTTAACGGTTTATTGGCTGAACAACTGGAAGCACGATTGACTGGCGCTACACCGCCAGATACCggg > 1:3213477/1‑69 (MQ=255)
ccGTTTAACGGTTTATTGGCTGAACAACTGGAAGCACGATTGACTGGCGCTACACCGCCAGATACCggg > 1:3217419/1‑69 (MQ=255)
tAACGGTTTATTGGCTGAACAACTGGAAGCACGATTGACTGGCGCTACACCGCCAGATACCGGGAtttt > 1:3036924/1‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGATTTTTCGGt > 1:1880839/3‑40 (MQ=37)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGTTATCATGAAATATGTGCCGCGaa > 1:881152/3‑62 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATc > 1:2616039/3‑64 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:3262900/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:410075/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:522140/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:3129426/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:3120298/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:961801/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:2934687/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:2751621/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:2445479/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:1038603/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:1461720/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:2366245/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:2291186/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:2268504/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:1660245/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:2162924/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:2053030/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:173715/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:2440658/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:1884772/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:1761453/3‑69 (MQ=255)
actGACTGGCGCTACACCGCCAGATACCGGAATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGaa > 1:1790109/3‑69 (MQ=255)
tGGCGCTACACCGCCAGATACCGGGATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGAAAcgcg < 1:1926389/68‑1 (MQ=255)
tGGCGCTACACCGCCAGATACCGGGATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGAAAcgcg < 1:3434083/68‑1 (MQ=255)
tGGCGCTACACCGCCAGATACCGGGATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGAAAcgcg < 1:1840412/68‑1 (MQ=255)
tGGCGCTACACCGCCAGATACCGGGATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGAAAcgcg < 1:3138164/68‑1 (MQ=255)
tGGCGCTACACCGCCAGATACCGGGATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGAAAcgcg < 1:2249189/68‑1 (MQ=255)
tGGCGCTACACCGCCAGATACCGGGATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGAAAcgcg < 1:247104/68‑1 (MQ=255)
tGGCGCTACACCGCCAGATACCGGGATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGAAAcgcg < 1:1020326/68‑1 (MQ=255)
|
CCGTTTAACGGTTTATTGGCTGAACAACTGGAAGCACGATTGACTGGCGCTACACCGCCAGATACCGGGATTTTCGGTATCATGAAAGATGTGCCGCGAATCATGAAACGCG > minE/1584824‑1584935
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
