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 |
1,371,355 |
G→A |
40.2% |
L161L (CTG→CTA) |
cdd → |
cytidine/deoxycytidine deaminase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,371,355 | 0 | G | A | 40.2%
| 29.4
/ 44.5
| 67 | L161L (CTG→CTA) | cdd | cytidine/deoxycytidine deaminase |
| Reads supporting (aligned to +/- strand): ref base G (3/37); new base A (18/9); total (21/46) |
| Fisher's exact test for biased strand distribution p-value = 3.71e-07 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.30e-01 |
CAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATGGACGAACAGGATCACGGC > minE/1371292‑1371421
|
cAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCa < 1:1528345/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:2759026/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:1813608/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:1626343/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:2243955/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:108341/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:410967/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:447380/67‑1 (MQ=255)
tCTGCGTATTCATCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:940694/67‑1 (MQ=255)
tGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGcc > 1:2176163/1‑67 (MQ=255)
aTTCATCTGTCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:64799/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:355729/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:2478277/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:811982/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:2063675/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:1961022/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:948735/69‑1 (MQ=255)
aTTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGAt < 1:1251363/69‑1 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCtttc > 1:351830/1‑53 (MQ=37)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTg > 1:663541/1‑54 (MQ=37)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTGGGCCGATAGAtgaa > 1:2598403/1‑65 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGAtgaa > 1:802633/1‑65 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGAtgaa > 1:1957893/1‑65 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGAtgaa > 1:1168612/1‑65 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGAtgaa > 1:1705631/1‑65 (MQ=255)
aTCTTCCGGGACGCGAGGCACACGCGCTGCGTGACTATATACCGGATg > 1:1541863/1‑48 (MQ=21)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCTGAAAGATCTGGAGATTaa < 1:702012/69‑1 (MQ=255)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTaa < 1:1791553/69‑1 (MQ=255)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTaa < 1:604470/69‑1 (MQ=255)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTaa < 1:548019/69‑1 (MQ=255)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTaa < 1:822774/69‑1 (MQ=255)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTaa < 1:2486332/69‑1 (MQ=255)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTaa < 1:139283/69‑1 (MQ=255)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTaa < 1:1996308/69‑1 (MQ=255)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTa < 1:2617811/68‑1 (MQ=255)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTa < 1:2075436/68‑1 (MQ=255)
gggCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTa < 1:1305727/68‑1 (MQ=255)
gcgAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACgc < 1:530137/69‑1 (MQ=255)
ggCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACgctgct < 1:2688929/69‑1 (MQ=255)
ggCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACgctgct < 1:1324554/69‑1 (MQ=255)
ggCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACgctgct < 1:584926/69‑1 (MQ=255)
ggCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACgctgct < 1:3029397/69‑1 (MQ=255)
ggCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACgctgct < 1:526229/69‑1 (MQ=255)
gCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACgctgct < 1:1920295/68‑1 (MQ=255)
cacGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACgctgct < 1:3431951/65‑1 (MQ=255)
acGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACgctgct < 1:1883786/64‑1 (MQ=255)
acGCGCTGCGTGACTATCTACCGGATGCCTTTggg < 1:2629177/35‑1 (MQ=37)
cgcgCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:2428182/1‑68 (MQ=255)
cgcgCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:3283735/1‑68 (MQ=255)
cgcgCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACg > 1:3237705/1‑58 (MQ=255)
cgcgCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:1399728/1‑68 (MQ=255)
cgcgCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:3251706/1‑68 (MQ=255)
cgcgCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:2112486/1‑68 (MQ=255)
cgcgCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:1152567/1‑68 (MQ=255)
cgcgCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:2804138/1‑68 (MQ=255)
cgcgCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:2775823/1‑68 (MQ=255)
cgcgCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:1723526/1‑68 (MQ=255)
cgcgCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:2419471/1‑68 (MQ=255)
cgcgCTGCGTGACTATCTACCGGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATgg > 1:2433870/1‑68 (MQ=255)
cTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATGGACGaa < 1:1197650/69‑1 (MQ=255)
cTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATGGACGaa < 1:1090823/69‑1 (MQ=255)
tATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACgctgct < 1:1731425/50‑1 (MQ=255)
tGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATGGACGaa < 1:3184252/56‑1 (MQ=255)
tGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATGGACGaa < 1:300420/56‑1 (MQ=255)
tGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATGGACGaa < 1:2408930/56‑1 (MQ=255)
tGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATGGACGAACAGGATCACGGc < 1:698340/68‑1 (MQ=255)
tGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATGGACGAACAGGATCACGGc < 1:1131200/68‑1 (MQ=255)
|
CAGCGGTCTGGATCTGCGTATTCATCTGCCGGGCCGCGAGGCACACGCGCTGCGTGACTATCTGCCAGATGCCTTTGGGCCGAAAGATCTGGAGATTAAAACGCTGCTGATGGACGAACAGGATCACGGC > minE/1371292‑1371421
|
| 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
