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 F8 I0 R1
|
82 |
77.9 |
2158605 |
86.8% |
1873669 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
840,460:1 |
+T |
100% |
coding (352/459 nt) |
ychJ ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 840,460 | 1 | . | T | 77.3%
| 124.8
/ 32.0
| 44 | coding (352/459 nt) | ychJ | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (10/0); new base T (34/0); total (44/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.07e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
CGTTGCGACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTC‑TTTCAAAAATCGCGAACGTTCAATTATTGCACCTGTTTTACCACCTTCGGTAAATCG > minE/840406‑840517
|
cGTTGCGACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTC‑TTTCaaaa > 1:142569/1‑63 (MQ=255)
cGTTGCGACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTC‑TTTCAAAAATc > 1:2075645/1‑66 (MQ=255)
cGTTGCGACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTC‑TTTCAAAAATc > 1:1321010/1‑66 (MQ=255)
cGTTGCGACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTC‑TTTCAAAAATc > 1:1348257/1‑66 (MQ=255)
cGTTGCGACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTC‑TTTCAAAAATc > 1:1383082/1‑66 (MQ=255)
cGTTGCGACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTC‑TTTCAAAAATc > 1:2007795/1‑66 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATcgcg > 1:566534/1‑64 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATc > 1:1822673/1‑61 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGaa > 1:908207/1‑66 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGaa > 1:483534/1‑66 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:290746/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:34885/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:292294/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:549301/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:284318/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:2148509/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:2142648/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:385548/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:508194/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:2062964/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:611833/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:750575/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:861711/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:873538/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:974755/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:2124723/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:1173161/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:2039230/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:2023765/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:1991590/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:1950905/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:1860996/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:1838195/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:1697692/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:122776/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:1641289/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:1435916/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:1380198/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:1352780/1‑67 (MQ=255)
gACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTCTTTTCAAAAATCGCGAAc > 1:124371/1‑67 (MQ=255)
gACCGTTTTC‑TTTCAAAAATCGCGAACGTTCAATTATTGCACCTGTTTTACCACCTTCGGTAAATCg > 1:1170741/1‑67 (MQ=255)
gACCGTTTTC‑TTTCAAAAATCGCGAACGTTCAATTATTGCACCTGTTTTACCACCTTCGGTAAATCg > 1:2156945/1‑67 (MQ=255)
gACCGTTTTC‑TTTCAAAAATCGCGAACGTTCAATTATTGCACCTGTTTTACCACCTTCGGTAAATCg > 1:1115143/1‑67 (MQ=255)
gACCGTTTTC‑TTTCAAAAATCGCGAACGTTCAATTATTGCACCTGTTTTACCACCGTCGGTAAATCg > 1:523448/1‑67 (MQ=255)
|
CGTTGCGACCAAACTGCGGACGTGTACCGTCAATATAGTACCATTGACCGTTTTC‑TTTCAAAAATCGCGAACGTTCAATTATTGCACCTGTTTTACCACCTTCGGTAAATCG > minE/840406‑840517
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
