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 F4 I96 R1
|
227 |
23.3 |
882352 |
98.0% |
864704 |
126.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
885,786 |
T→G |
L81R (CTG→CGG) |
ybjM → |
inner membrane protein YbjM |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 885,786 | 0 | T | G | 94.7%
| 60.0
/ ‑2.4
| 19 | coding (242/378 nt) | ybjM | inner membrane protein YbjM |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base G (7/11); minor base . (0/1); total (7/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.11e-01 |
TCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCTGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCA > NZ_CP009273/885678‑885906
|
tCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGc < 1:157945/138‑1 (MQ=255)
ttcCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCt > 2:294489/1‑139 (MQ=255)
cTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTgg < 1:175544/138‑1 (MQ=255)
gTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGC‑GGTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACt < 2:258496/139‑1 (MQ=255)
tCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACt < 1:21220/139‑1 (MQ=255)
tCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACt < 1:341132/139‑1 (MQ=255)
cttcttTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGcgcg < 1:58867/139‑1 (MQ=255)
caGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGgt < 2:306222/139‑1 (MQ=255)
cGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTGCTAAGCGCGGTGTTCTGGggtg > 2:51695/1‑139 (MQ=255)
gaAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTgg < 1:86350/139‑1 (MQ=255)
gTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTggggg < 1:316770/139‑1 (MQ=255)
tCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTggggg > 2:6196/1‑138 (MQ=255)
cTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCTCTGGGGGCAc < 1:188344/139‑1 (MQ=255)
gAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACtg > 2:243642/1‑139 (MQ=255)
cgcAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGGCGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAgcg > 2:195951/1‑95 (MQ=255)
cgcAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAgcg < 1:195951/95‑1 (MQ=255)
gcggcACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGTGCTGGCCTGGTTACTAAGCGCGGTGtt > 1:189603/1‑92 (MQ=255)
gcggcACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGtt < 2:189603/92‑1 (MQ=255)
tGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCCAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACcacagca > 1:60096/1‑136 (MQ=255)
|
TCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCTGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCA > NZ_CP009273/885678‑885906
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCTGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCAC > NZ_CP009273/885677‑885907
|
TTCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCA < SRR3722119.159558/150‑1 (MQ=60)
CCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTA < SRR3722119.177345/150‑1 (MQ=60)
GTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGT < SRR3722119.21419/151‑1 (MQ=60)
GTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGT < SRR3722119.344612/151‑1 (MQ=60)
gtctcgtgggctcggagatgtgtataagagacagCCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTGCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGG < SRR3722119.198044/117‑1 (MQ=60)
GCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTG < SRR3722119.59413/151‑1 (MQ=60)
GCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACCCGCTCCTTCTTGCCAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTtgctgtctcttatacac > SRR3722119.301155/1‑134 (MQ=60)
AGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGT < SRR3722119.87201/151‑1 (MQ=60)
AGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTC < SRR3722119.320010/151‑1 (MQ=60)
CCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCTCTGGGGGCACTGTGTTTCTTA < SRR3722119.190320/151‑1 (MQ=60)
GCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCAAGTGCTGGCCTGGTTACTAAGCGCGGGGTTCTGGTGTGtgcctgtctcttatacacccatccgagcgcacgagacta > SRR3722119.191598/1‑111 (MQ=60)
ACCCTGTTCGATGCTCATTATGCGGCGGTTTTTTTCACCGACGCGCTCATTCTGGCCAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCAC > SRR3722119.60657/1‑148 (MQ=60)
|
TTCATTCTTCCTGGAGCAGTCGCCAGCTTCTTTTCACAGCGTAGAGAAGTCCTGAAACCTCTGTTTGGCGCAATGCTGGCGGCACCCTGTTCGATGCTCATTATGCGGCTGTTTTTTTCACCGACGCGCTCATTCTGGCAAGAGCTGGCATGGTTACTAAGCGCGGTGTTCTGGTGTGCGCTGGGGGCACTGTGTTTCTTATTTATCAGTAGTTTGTTTAAACCACAGCAC > NZ_CP009273/885677‑885907
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
