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 |
|
A13 F56 I0 R1
|
198 |
55.3 |
2323794 |
95.3% |
2214575 |
126.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP006881 |
3,725,239 |
2 bp→AA |
100% |
intergenic (‑71/‑457) |
U712_19205 ← / → U712_19210 |
Uncharacterized protein ywcI/Minor extracellular protease vpr |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP006881 | 3,725,239 | 0 | G | A | 99.1%
| 106.8
/ ‑6.7
| 32 | intergenic (‑71/‑458) | U712_19205/U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (18/13); minor base C (1/0); total (19/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| 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. |
| * | CP006881 | 3,725,240 | 0 | G | A | 100.0%
| 97.3
/ ‑6.6
| 32 | intergenic (‑72/‑457) | U712_19205/U712_19210 | Uncharacterized protein ywcI/Minor extracellular protease vpr |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (19/12); minor base T (0/1); total (19/13) |
| 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. |
TTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑TTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAG > CP006881/3725119‑3725363
||
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCGGAtt > 8:78097/1‑139 (MQ=255)
catcaAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtttc > 4:81683/1‑139 (MQ=255)
aTCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCaaa > 8:187875/1‑138 (MQ=255)
tCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCCAAc > 4:240591/1‑138 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAAGATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCGGCCCGTTTTCTCAGCCGCAGCCCGCAACAAACGAAGGCCGATTTCTTTTATCGCAAACTACCGGctc > 7:140166/1‑137 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTGGCAGCCCGGTTTCTCAGCCGCCGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACTAGCGGctc > 8:118372/1‑137 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctc > 7:173841/1‑137 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCATTTATCGCAAACTAGCGGctg > 3:31481/1‑136 (MQ=255)
tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCCAGAAAAGACGGCCGAGTTCTTTTAGCGCCAACAATCGGcgcaa > 4:14852/1‑135 (MQ=255)
aaGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAg > 3:108276/1‑138 (MQ=255)
ctaTACAACCAACCTTTTAATACAAAAACAACCCTCCGCTTCTTTTTGGCAGGCAGCTT‑TTTTCGCAGCCCTTTTCCTCCGCCGCAGCCCCAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 8:173841/137‑1 (MQ=255)
aGATACACGAAAACGTTTCATAGAAAAACACCCCTCCGCTTCTTTTTCGCCGCCAGCGT‑TTTTCGCAGCCCGTTTTCTCAGCCGCACCCCGCAACAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 7:118372/139‑1 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCaaaa > 6:107549/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCaaaa > 7:19065/1‑138 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAAc > 5:24653/1‑139 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAAc > 5:289979/1‑139 (MQ=255)
aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTATCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTACTTTTCTCGCAAACTACCGGCTCTAGCaaaa > 8:187100/1‑138 (MQ=255)
gaaacggTTTCATCTAAAAACATCCCTCCGATTCTTTTTGGCTGGCAGCTT‑TTTTCGCAGCGCGTTTTCTCAGCCGCAGCCCGAAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt < 7:187100/133‑1 (MQ=255)
gCAAACGTTTCATATAAAACCACCCCTCCGCTTCTTTTTGCCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCCGCCCCAGCCCGCAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt < 3:81683/139‑1 (MQ=255)
ccAAACTTTTCATAAAAAAACATCCCACCGCTTCTTTTTGCCAGGAAGC‑CTTTTTCTCACCCGGTTTTCTCCGCCGCCGCCCCCAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt < 3:240591/138‑1 (MQ=255)
aaCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGAAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAc < 7:187875/139‑1 (MQ=255)
acttttCATAAAAAAACATCCCTCCGCTTCTTTTTGGCCGGCAGCTT‑TTTTAGCCGCCCGTTTTCTCAGCCGCCGCCCGAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 4:108276/136‑1 (MQ=255)
aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 5:107549/139‑1 (MQ=255)
aCGTTTAATATAAAAAAATCCATCGGCTTATTTTTGGATGGCAGCGT‑TTTTTGATCCCCTTTTTCTCAGCCCCAGCCCGAATTAAAAGACGGCCGATTTCTTTTCTCGAAAACTAGCGGCTCTAGCAAAACTCATGAct < 8:19065/139‑1 (MQ=255)
aCGTTACAAACAAAAACATCCCACCGCTTCTTTTTGGCAGGCACC‑CTTTTTAGCCCCCGGTTTGCTCAGCCCCCGCCCCCAACAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct < 7:177750/139‑1 (MQ=255)
aaaaaCATCCCTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGAc < 6:289979/139‑1 (MQ=255)
cTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa < 7:72249/106‑1 (MQ=255)
cTCCGCTTCTTTTTGGCAGGCAGC‑CTTTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa > 8:72249/1‑106 (MQ=255)
cGCTTCTTTTTGGCCGGCCGC‑CTTTTTCGCAGCCCGTTTCCTCAGCCGCAGCCCCCAACAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGaa < 6:120890/139‑1 (MQ=255)
gcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCaa > 3:40210/1‑139 (MQ=255)
cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAAc > 5:272717/1‑139 (MQ=255)
cAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTTTGACAATATTAGTTAAAAAACCAACTAGttttttg > 7:263232/1‑137 (MQ=255)
||
TTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAGC‑C‑TTTTAGCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAG > CP006881/3725119‑3725363
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
