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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,380 |
2 bp→AA |
100% |
pseudogene (513‑514/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,380 | 0 | G | A | 100.0%
| 175.0
/ NA
| 61 | pseudogene (513/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (34/27); total (34/27) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | W3110S.gb | 3,824,381 | 0 | G | A | 98.4%
| 165.8
/ ‑4.2
| 61 | pseudogene (514/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (33/27); total (34/27) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-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. |
GAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCG > W3110S.gb/3824317‑3824444
||
gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:1521820/1‑70 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt > 1:923239/1‑71 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAG‑CGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc > 1:3602103/1‑71 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt > 1:655273/1‑71 (MQ=255)
cGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:75869/1‑68 (MQ=255)
gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc < 1:1414724/58‑1 (MQ=255)
gATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg < 1:2579716/71‑1 (MQ=255)
aTGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGt > 1:204080/1‑71 (MQ=255)
tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt < 1:536567/71‑1 (MQ=255)
tGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt < 1:341784/71‑1 (MQ=255)
aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg > 1:1311301/1‑70 (MQ=255)
aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:3354893/70‑1 (MQ=255)
aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:4179312/71‑1 (MQ=255)
gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:1607866/69‑1 (MQ=255)
gggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:2836500/69‑1 (MQ=255)
ggATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAc < 1:343071/71‑1 (MQ=255)
gATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct < 1:443965/71‑1 (MQ=255)
tGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:3845400/54‑1 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:3980273/1‑71 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:302832/1‑71 (MQ=255)
tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:820791/45‑1 (MQ=25)
tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc > 1:264769/1‑71 (MQ=255)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:724100/1‑68 (MQ=255)
cGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:4445335/1‑68 (MQ=255)
cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACg > 1:2506905/1‑51 (MQ=255)
cAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa > 1:3491147/1‑68 (MQ=255)
gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc < 1:1465387/36‑1 (MQ=16)
gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc > 1:3924004/1‑71 (MQ=255)
tttCTGTCTGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAca < 1:4383232/71‑2 (MQ=255)
tttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:3461261/42‑1 (MQ=19)
tttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg < 1:1541307/63‑1 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAg > 1:4563948/1‑52 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActc > 1:1011130/1‑56 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:973091/1‑59 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag > 1:3623071/1‑66 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:2337851/1‑71 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATAAGTTGAAGActc > 1:3448351/1‑56 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:1676582/1‑70 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:1968961/1‑70 (MQ=255)
gTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:4549823/1‑39 (MQ=16)
gTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:287726/1‑39 (MQ=16)
gTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGAc > 1:1331496/1‑69 (MQ=255)
tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg < 1:3662472/71‑1 (MQ=255)
cGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATg > 1:3417052/1‑70 (MQ=255)
ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:3695592/4‑71 (MQ=255)
ggtaTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGaa > 1:562478/4‑71 (MQ=255)
taTTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:2140886/42‑1 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:891547/39‑1 (MQ=21)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:2990213/41‑1 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActcag < 1:3425114/48‑3 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActcag < 1:3309341/48‑3 (MQ=25)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg < 1:357173/51‑1 (MQ=255)
ttGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGAc > 1:675131/1‑62 (MQ=255)
gtaaaCGGTGAAGCAGTTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:3019551/4‑71 (MQ=255)
gtaaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt > 1:3517319/4‑71 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTTGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt < 1:2654906/68‑1 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGt < 1:3041565/68‑1 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat > 1:4074333/1‑71 (MQ=255)
aaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat > 1:3138434/1‑71 (MQ=255)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg < 1:487381/70‑1 (MQ=255)
tgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCg < 1:2761148/70‑1 (MQ=255)
||
GAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCG > W3110S.gb/3824317‑3824444
|
| 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
