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 |
|
A7 F80 I0 R1
|
1148 |
65.4 |
3296958 |
93.8% |
3092546 |
131.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947 |
5,222,953 |
G→C |
61.5% |
intergenic (‑316/+63) |
PP_4602 ← / ← PP_4603 |
AraC family transcriptional regulator/transposase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947 | 5,222,953 | 0 | G | C | 61.5%
| 3.1
/ 12.2
| 13 | intergenic (‑316/+63) | PP_4602/PP_4603 | AraC family transcriptional regulator/transposase |
| Reads supporting (aligned to +/- strand): ref base G (3/2); new base C (5/3); total (8/5) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.81e-01 |
TTTCCCGCGCATTGGGAACCATAGCAAAGTATTCGGCGGCTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCATCAAACAAAATGCAACCCATTGTTTTCTAAGCACTCAAGCGGCCACCAGTTGATACCCCAGTTTCCGGGCTTTGCGAAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGG > NC_002947/5222821‑5223092
|
gagttcgaagccagaagccaagaccggcaggtccgggctttgcttcgcaaagcccggaaactggggtatcaactggtggccgcttgagtgcttagaaaacaatgggttgcattttgtttgatgagagatcaCCCAGCCCGGAAGGGCTgg > 2:1131223‑M1/132‑150 (MQ=255)
agttcgaagccagaagccaagaccggcaggtccgggctttgcttcgcaaagcccggaaactggggtatcaactggtggccgcttgagtgcttagaaaacaatgggttgcattttgtttgatgagagatcaCCCAGCCCGGAAGGGCTggg > 2:1537833‑M1/131‑150 (MQ=255)
agaagccaagaccggcaggtccgggctttgcttcgcaaagcccggaaactggggtatcaactggtggccgcttgagtgcttagaaaacaatgggttgcattttgtttgctgtgcgacagCGCAGCCCGGAAGGGCTGGGTGATCTCtcat < 1:146898‑M1/31‑1 (MQ=255)
gaagccaagaccggcaggtccgggctttgcttcgcaaagcccggaaactggggtatcaactggtggccgcttgagtgcttagaaaacaatgggttgcattttgtttgatgagagatcaCCCAGCCCGGAAg < 1:1469375‑M1/13‑1 (MQ=255)
gaagccaagaccggcaggtccgggctttgcttcgcaaagcccggaaactggggtatcaactggtggccgcttgagtgcttagaaaacaatgggttgcattttgtttgatgagagatcaCCCAGCCCGGAAg > 2:1469375‑M1/119‑131 (MQ=255)
ccaagaccggcaggtccgggctttgcttcgcaaagcccggaaactggggtatcaactggtggccgcttgagtgcttagaaaacaatgggttgcattttgtttgctgtgcgacagCGCAGCCCGGAAGGGCTGGGTGATCTCTCATcaaac > 2:146898‑M1/115‑150 (MQ=255)
cgggcttggcgaagcaaagcccggaaactggggtatcaactggtggccgcttgagtgcttagaaaacaatgggttgcattttgtttgatgagagatcaCGCAGCCCGGAAGGGCTGGGTGATCTCtcatc > 2:714785‑M1/99‑130 (MQ=255)
ggggtatcaactggtggccgcttgagtgcttagaaaacaatgggttgcattttgtttgatgagagatcaCGCAGCCCGGAAGGGCTGGGTGAtc < 1:20353‑M1/25‑1 (MQ=255)
ggggtatcaactggtggccgcttgagtgcttagaaaacaatgggttgcattttgtttgatgagagatcaCGCAGCCCGGAAGGGCTGGGTGAtc > 2:20353‑M1/70‑94 (MQ=255)
ggccgcttgagtgcttagaaaacaatgggttgcattttgtttgatgagagatcaCCCAGCCCGGAAGGGCTGGGt < 1:1070503‑M1/21‑1 (MQ=255)
ggccgcttgagtgcttagaaaacaatgggttgcattttgtttgatgagagatcaCCCAGCCCGGAAGGGCTGGGt > 2:1070503‑M1/55‑75 (MQ=255)
gatgagagatcaCCCAGCCCTTCCGGGCTGCGTGATCTCTCATCAAACAAAATGCAACCCATTGTTTTCTAAGCACTCAAGCGGCCACCAGTTGATACCCCAGTTTCCGGGCTTTGCTTCGCAAAGCCCg > 1:714785‑M1/13‑130 (MQ=255)
gagagatcaCCCAGCCCTTCCGGGCTGCGTGATCTCTCATCAAACAAAATGCAACCCATTGTTTTCTAAGCACTCAAGCGGCCACCAGTTGATACCCCAGTTTCCGGGCTTTGCGAAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTgg < 1:275861‑M1/141‑1 (MQ=255)
|
TTTCCCGCGCATTGGGAACCATAGCAAAGTATTCGGCGGCTGACCTACCCGGATCAGTCGGCGAATGCTTTTCTAGATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCTCATCAAACAAAATGCAACCCATTGTTTTCTAAGCACTCAAGCGGCCACCAGTTGATACCCCAGTTTCCGGGCTTTGCGAAGCAAAGCCCGGACCTGCCGGTCTTGGCTTCTGG > NC_002947/5222821‑5223092
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
