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 |
|
A6 F28 I2 R2
|
64 |
60.0 |
3197630 |
92.7% |
2964203 |
60.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
minE |
1,230,834 |
+A |
coding (1922/2061 nt) |
ptrB ← |
protease II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,230,830 | 1 | . | A | 97.7%
| 140.3
/ ‑2.7
| 43 | coding (1926/2061 nt) | ptrB | protease II |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base A (17/25); total (18/25) |
| Fisher's exact test for biased strand distribution p-value = 4.19e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
CGCCTTCGTACGATTTAAAGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAAT‑AAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGCCGGTTCCCAA > minE/1230763‑1230890
|
cGCCTTCGTACGATTTAAAGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAAT‑aaa < 1:2000777/71‑1 (MQ=255)
gCCTTCGTACGATTTAAAGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAAT‑aaa > 1:225317/1‑70 (MQ=255)
gCCTTCGTACGATTTAAAGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAAT‑a < 1:959465/68‑1 (MQ=255)
gCCTTCGTACGATTTAAAGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAAT‑a < 1:2954272/68‑1 (MQ=255)
cTTCGTACGATTTAAAGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAAT‑aaaaag < 1:1221345/71‑3 (MQ=255)
cGTACGATTTAAAGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAAT‑aaaaaga < 1:1936726/69‑4 (MQ=255)
gATTTAAAGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCAt > 1:242133/1‑71 (MQ=255)
aaaGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGtt > 1:202679/1‑71 (MQ=255)
aaaGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAAT‑AAAAGATGGTCATCGGttt > 1:2014230/1‑71 (MQ=255)
aaaGCGACCAGATTTACCGCCATGGCCTGACTCCATGTCGGTACAGCGCAATAAAAAGATGGTCATCGGtt > 1:429634/1‑71 (MQ=255)
aaGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGttt < 1:1802938/71‑1 (MQ=255)
aGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGtttt > 1:545779/1‑71 (MQ=255)
aGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGtttt < 1:176293/71‑1 (MQ=255)
gACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCa < 1:2719977/70‑1 (MQ=255)
aCCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGc < 1:3148113/71‑1 (MQ=255)
ccAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCt < 1:3020045/71‑1 (MQ=255)
ccAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGGCATCGGTTTTCAGCt < 1:904305/71‑1 (MQ=255)
cAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAAt > 1:1400361/1‑44 (MQ=255)
cAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTc < 1:2973055/71‑1 (MQ=255)
gATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCTATAAAAAGATGGTCATCGGTTTTCAGCTcgc < 1:2689846/71‑1 (MQ=255)
gATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTcgc < 1:730033/71‑1 (MQ=255)
aTTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTcgc > 1:1613700/1‑70 (MQ=255)
aCCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAAt > 1:3136579/1‑71 (MQ=255)
ccGCCATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGttt < 1:1638126/56‑1 (MQ=255)
cATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGc > 1:1150742/1‑71 (MQ=255)
cATGGCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGc < 1:2326013/71‑1 (MQ=255)
gCCTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGAcc < 1:1751950/71‑1 (MQ=255)
ccTGAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGAcc > 1:2912979/1‑70 (MQ=255)
gAGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCAtt > 1:2369812/1‑71 (MQ=255)
aGTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCAtt < 1:2135506/70‑1 (MQ=255)
gTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATc > 1:1892340/1‑37 (MQ=38)
gTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATc > 1:2017093/1‑37 (MQ=38)
gTCCATGTCGGTACAGAGCAATAAAAAGATGGTCATc > 1:157292/1‑37 (MQ=38)
tCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCAt < 1:821636/67‑1 (MQ=255)
tCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCAt < 1:164113/67‑1 (MQ=255)
tCCATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCAt < 1:520673/67‑1 (MQ=255)
cATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGtt < 1:2982189/38‑1 (MQ=38)
cATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGtt < 1:456307/38‑1 (MQ=38)
cATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGcc < 1:1592364/71‑1 (MQ=255)
cATGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGAGCAATTTAGCGACCCATTTTGcc < 1:2678630/71‑1 (MQ=255)
tGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTcg > 1:133471/1‑45 (MQ=255)
tGTCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTcg > 1:288108/1‑45 (MQ=255)
tCGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGCCGGt < 1:2782391/70‑1 (MQ=255)
cGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGCCGGTTc > 1:2835199/1‑71 (MQ=255)
cGGTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGCCGGTTc > 1:2507732/1‑71 (MQ=255)
ggTACAGAGCAATAAAAAGATGGGCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGCCggg < 1:2361260/68‑2 (MQ=255)
gTACAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGc < 1:2451488/63‑1 (MQ=255)
aCAGAGCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGCCGGTTc > 1:537677/1‑67 (MQ=255)
agCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGCCGGTTCCCaa < 1:2921072/67‑1 (MQ=255)
agCAATAAAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGCCGGTTCCCaa < 1:41/67‑1 (MQ=255)
|
CGCCTTCGTACGATTTAAAGCGACCAGATTTACCGCCATGGCCTGAGTCCATGTCGGTACAGAGCAAT‑AAAAGATGGTCATCGGTTTTCAGCTCGCGCAATTTAGCGACCCATTTTGCCGGTTCCCAA > minE/1230763‑1230890
|
| 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
