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 |
|
A5 F3 I0 R2
|
52 |
68.8 |
5189613 |
98.4% |
5106579 |
62.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,093,686 |
T→C |
100% |
V130A (GTA→GCA) |
ycdT → |
predicted diguanylate cyclase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,093,686 | 0 | T | C | 98.2%
| 181.8
/ ‑4.5
| 54 | V130A (GTA→GCA) | ycdT | predicted diguanylate cyclase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (27/26); minor base G (1/0); total (28/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTTGT > W3110S.gb/1093622‑1093751
|
cAAAATGACATTGCAATATATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGt < 1:2562907/71‑1 (MQ=255)
aaTGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGaa > 1:4270430/1‑71 (MQ=255)
aTGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAAt < 1:3226353/71‑1 (MQ=255)
tGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGAATATTAATATTTCTGGCATTGGTGAAt > 1:5052623/1‑70 (MQ=255)
gCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAg > 1:4957723/1‑71 (MQ=255)
cAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAg < 1:1778820/70‑1 (MQ=255)
aaTCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTg < 1:160673/71‑1 (MQ=255)
tattatTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaaaa > 1:4656759/1‑71 (MQ=255)
attattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTgg > 1:1085215/1‑51 (MQ=255)
ttattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaa < 1:3924639/67‑1 (MQ=255)
tattTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAg > 1:520061/1‑58 (MQ=255)
attTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAacac > 1:4709542/1‑70 (MQ=255)
tGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa > 1:3847830/1‑71 (MQ=255)
tGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa > 1:291230/1‑71 (MQ=255)
tGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaa > 1:2159413/1‑70 (MQ=255)
gTTTCGTCAGATGAGTTTGTTCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaaa < 1:1752324/70‑1 (MQ=255)
tttCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGtt < 1:2817519/54‑1 (MQ=255)
ttCGTCAGATGAGTTTGTGCATATTAATATTTCTGGCAtt > 1:2085144/1‑40 (MQ=255)
cGTCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAgcg > 1:993245/1‑71 (MQ=255)
gTCAGATGAGTTTGTGCATATTAATATTTCTGGCAt < 1:4236818/36‑1 (MQ=255)
tCAGATGAGTTTGTGCATATTAATATTTCTGGCAt < 1:2388543/35‑1 (MQ=255)
tCAGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAAt < 1:831548/43‑1 (MQ=255)
aGATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCaa < 1:4948783/70‑1 (MQ=255)
gATGAGTTTGTGCATATTAATATTTCTGGCATTGGTGaa > 1:3868517/1‑39 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAAc < 1:449576/61‑1 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAattt < 1:519367/71‑1 (MQ=255)
aTGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatt > 1:638651/1‑70 (MQ=255)
tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTa > 1:3516019/1‑45 (MQ=255)
tGAGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTa > 1:2260036/1‑45 (MQ=255)
aGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttat < 1:854010/70‑1 (MQ=255)
aGTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttat < 1:2035682/70‑1 (MQ=255)
gTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttattt < 1:4711518/71‑1 (MQ=255)
gTTTGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAatttattt < 1:452290/71‑1 (MQ=255)
tttGTGCATATTAATATTTCTGGCATTGGTGAATaa < 1:57838/36‑1 (MQ=255)
tttGTGCATATTAATATTTCTGGCATTGGTGAATaa < 1:4301126/36‑1 (MQ=255)
tttGTGCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTAtttt < 1:1583859/71‑1 (MQ=255)
tgtgCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGt > 1:2722069/1‑41 (MQ=255)
tgtgCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGt > 1:55268/1‑41 (MQ=255)
gCATATTAATATTTCTGGCATTGGTGAATAAAGTTAGTGaa < 1:2474632/41‑1 (MQ=255)
atatTAATATTTCTGGCATTGGTGAATAAAGTTAg > 1:4280540/1‑35 (MQ=255)
atatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaa > 1:4777892/1‑70 (MQ=255)
tatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaa > 1:910976/1‑70 (MQ=255)
tatTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaa > 1:394261/1‑70 (MQ=255)
atTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACa < 1:820434/48‑1 (MQ=255)
atTAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaaaaaa > 1:443903/1‑71 (MQ=255)
ttAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAAt < 1:4156007/71‑1 (MQ=255)
tAATATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCaaa < 1:4059643/65‑1 (MQ=255)
aaTATTTCTGGGATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGa > 1:4917119/1‑71 (MQ=255)
aaTATTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGa > 1:2590203/1‑71 (MQ=255)
atatTTCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGa < 1:1565817/70‑1 (MQ=255)
tttCTGGCATTGGTGAATAAAGTTAGTGAAAACACaaa > 1:152654/1‑38 (MQ=255)
tCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTAtttt > 1:4572295/1‑53 (MQ=255)
tCTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTtgt > 1:3986621/1‑71 (MQ=255)
cTGGCATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTtgt < 1:5092300/70‑1 (MQ=255)
|
CAAAATGACATTGCAATCTATTATTTGTTTCGTCAGATGAGTTTGTGCATATTAATATTTCTGGTATTGGTGAATAAAGTTAGTGAAAACACAAAACAGCGCAATTTATTTTCCAAAAAAATGACTTTGT > W3110S.gb/1093622‑1093751
|
| 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
