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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,371,273 |
Δ2 bp |
100% |
intergenic (‑6/+299) |
dcuA ← / ← aspA |
C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,371,273 | 0 | A | . | 100.0%
| 159.1
/ NA
| 40 | intergenic (‑6/+300) | dcuA/aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (13/27); total (13/27) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | W3110S.gb | 4,371,274 | 0 | A | . | 100.0%
| 159.1
/ NA
| 40 | intergenic (‑7/+299) | dcuA/aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (13/27); total (13/27) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AGCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGAAAAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGG > W3110S.gb/4371218‑4371332
||
agcTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGTCAG‑‑AAATAGCGGCGATa < 1:2865955/69‑1 (MQ=255)
agcTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATa < 1:3159882/69‑1 (MQ=255)
agcTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATa < 1:3265238/69‑1 (MQ=255)
gcTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATa < 1:1479703/68‑1 (MQ=255)
ttCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGc > 1:2458702/1‑69 (MQ=255)
ctgtctgATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGc < 1:2244638/67‑1 (MQ=255)
tgatgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGa < 1:1173711/67‑1 (MQ=255)
tgatgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGAt < 1:6060/68‑1 (MQ=255)
tgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGAt > 1:856056/1‑65 (MQ=255)
tgaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGAt > 1:1028045/1‑65 (MQ=255)
gaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATaa > 1:1380110/1‑66 (MQ=255)
gaACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATaa > 1:548884/1‑66 (MQ=255)
aaCCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga < 1:447930/69‑1 (MQ=255)
aaCCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga < 1:716219/69‑1 (MQ=255)
aaCCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga < 1:3212165/69‑1 (MQ=255)
aaCCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga < 1:1008708/69‑1 (MQ=255)
aaCCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga < 1:915496/69‑1 (MQ=255)
aaCCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga < 1:2140304/69‑1 (MQ=255)
aaCCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga < 1:1656396/69‑1 (MQ=255)
aCCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGga < 1:2642381/68‑1 (MQ=255)
aGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATg < 1:2206756/69‑1 (MQ=255)
aGATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATg < 1:1162312/69‑1 (MQ=255)
gATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGAt < 1:53336/46‑1 (MQ=255)
gATAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGAt < 1:3565144/46‑1 (MQ=255)
aTAGTCCAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGAc < 1:3460558/69‑1 (MQ=255)
cAGACCGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGAt > 1:1102526/1‑51 (MQ=255)
ccGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGAt > 1:1135880/1‑56 (MQ=255)
ccGCCAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGAt > 1:1835620/1‑56 (MQ=255)
cAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGTATGt < 1:108693/69‑1 (MQ=255)
cAGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGt < 1:1872727/69‑1 (MQ=255)
aGCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGAt > 1:1845572/1‑42 (MQ=37)
gCAACCTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACgg > 1:3722275/1‑62 (MQ=255)
cTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCggg > 1:885608/1‑69 (MQ=255)
cTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCggg > 1:893247/1‑69 (MQ=255)
cTGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCggg > 1:2402207/1‑69 (MQ=255)
ttcATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACgg < 1:1732734/54‑1 (MQ=38)
tGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATTATAATGGAGATGACATCGAACGGGATGt < 1:3234098/61‑1 (MQ=255)
tGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACgg < 1:502656/56‑1 (MQ=38)
tGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACgg < 1:3512346/56‑1 (MQ=38)
tGCATGGCAG‑‑AAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACgg < 1:1942099/56‑1 (MQ=38)
||
AGCTTTTCTGTCTGATGAACCAGATAGTCCAGACCGCCAGCAACCTGCATGGCAGAAAAATAGCGGCGATAACCGCCATGATAATGGAGATGACATCGAACGGGATGTTACCGGG > W3110S.gb/4371218‑4371332
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
