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 |
|
A74 F1 I1 R1
|
16 |
49.9 |
3507628 |
96.2% |
3374338 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,145,965 |
T→C |
D34D (GAT→GAC) |
rpoD → |
RNA polymerase sigma factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,145,965 | 0 | T | C | 98.2%
| 219.4
/ ‑4.2
| 54 | D34D (GAT→GAC) | rpoD | RNA polymerase sigma factor |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (26/27); total (27/27) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01 |
ACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAA > REL606/3145893‑3146037
|
aCTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACAtc < 1:1543394/76‑1 (MQ=255)
tcttGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACAtcgtc > 1:1354959/1‑76 (MQ=255)
cttGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACAtcgtcg < 2:467888/76‑1 (MQ=255)
cttGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACAtcgtcg > 2:807814/1‑76 (MQ=255)
tCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATtc < 1:274836/76‑1 (MQ=255)
cACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATtca < 2:45564/76‑1 (MQ=255)
aCCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATtcag > 1:1389921/1‑76 (MQ=255)
aCCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATtcag > 1:1221577/1‑76 (MQ=255)
ccGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATtcagat > 1:1558652/1‑76 (MQ=255)
gTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTcagatcagat > 1:425368/1‑76 (MQ=255)
aaGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCg < 1:1111379/76‑1 (MQ=255)
aGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGa > 2:1261278/1‑76 (MQ=255)
aaGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGAcat < 1:1413531/76‑1 (MQ=255)
aaGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGAcat > 1:1539249/1‑76 (MQ=255)
aaGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGAcat > 1:1196160/1‑76 (MQ=255)
aaGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGAcat > 2:1004409/1‑76 (MQ=255)
aGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGAcatc > 2:888938/1‑76 (MQ=255)
gCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGAcatcat < 1:1243452/76‑1 (MQ=255)
cTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACatcatc > 2:481328/1‑76 (MQ=255)
tATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATcc > 2:271464/1‑76 (MQ=255)
tATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATcc > 1:1305286/1‑76 (MQ=255)
tATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATcc > 2:1026364/1‑76 (MQ=255)
aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCa > 2:1371136/1‑76 (MQ=255)
aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCa < 1:308795/76‑1 (MQ=255)
aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCa > 1:113358/1‑76 (MQ=255)
aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCa > 1:1232702/1‑76 (MQ=255)
aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGAGCGAAGACATCATCCa > 2:1371158/1‑76 (MQ=255)
tCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCaa < 1:220887/76‑1 (MQ=255)
gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATg < 1:447033/76‑1 (MQ=255)
gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATg > 2:218903/1‑76 (MQ=255)
gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATg < 1:878955/76‑1 (MQ=255)
ccTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGAt < 1:1446792/76‑1 (MQ=255)
ccTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGAt < 2:1479875/76‑1 (MQ=255)
gCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACg < 2:293784/76‑1 (MQ=255)
gAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACa > 1:1238666/1‑76 (MQ=255)
aTGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCAt < 2:1085156/76‑1 (MQ=255)
aTGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCAt < 2:719202/76‑1 (MQ=255)
aCCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCa < 2:1577167/76‑1 (MQ=255)
ccATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAg < 2:1524097/76‑1 (MQ=255)
ccATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAg > 2:206514/1‑76 (MQ=255)
cATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATCCAgg < 1:456260/76‑1 (MQ=255)
aTCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGt > 1:1199189/1‑76 (MQ=255)
tGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGAt < 1:1570530/76‑1 (MQ=255)
gCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATg > 2:1565922/1‑76 (MQ=255)
gCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATg > 2:844910/1‑76 (MQ=255)
ccGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATgg < 1:1599557/76‑1 (MQ=255)
cGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGga < 1:796652/76‑1 (MQ=255)
cGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGga > 1:1538694/1‑76 (MQ=255)
ggAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaa > 2:1731071/1‑76 (MQ=255)
ggAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaa > 2:1529733/1‑76 (MQ=255)
ggAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaa < 2:75661/76‑1 (MQ=255)
gAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCATATGATCAACGACATGGGCATTCAGGTGATGgaag < 1:1158095/76‑1 (MQ=255)
aaGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaaga < 2:995560/76‑1 (MQ=255)
aaGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaaga < 2:995563/76‑1 (MQ=255)
aGACATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaagaa < 1:1371253/76‑1 (MQ=255)
|
ACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAA > REL606/3145893‑3146037
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
