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 F2 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
674,442 |
T→G |
T141P (ACT→CCT) |
ybeT ← |
tetratricopeptide repeat protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 674,442 | 0 | T | G | 100.0%
| 46.3
/ NA
| 15 | T141P (ACT→CCT) | ybeT | tetratricopeptide repeat protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (8/7); total (8/7) |
TTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGTATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCAGACCTTTG > NZ_CP009273/674360‑674530
|
ttGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATtga < 1:396368/90‑1 (MQ=255)
gTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTgagcatgagcat < 2:175449/90‑1 (MQ=255)
gTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTgagcatgagcat < 2:385647/90‑1 (MQ=255)
tttttGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTc > 2:257577/1‑90 (MQ=255)
tCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTcc > 1:2640/1‑90 (MQ=255)
cATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCt < 2:390778/90‑1 (MQ=255)
tAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCaga > 2:31322/1‑90 (MQ=255)
aaCATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCagag > 1:387008/1‑90 (MQ=255)
ttAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAAtt < 1:265727/90‑1 (MQ=255)
aaTACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGc > 1:125907/1‑90 (MQ=255)
tGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTACACCAGAGAATTGCTTTACg > 1:132395/1‑90 (MQ=255)
gTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGttt > 1:287291/1‑90 (MQ=255)
tCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGAccc > 1:242337/1‑90 (MQ=255)
aCCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCAg < 2:2640/90‑1 (MQ=255)
aaGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGA‑‑CCCAGACCTTTg < 2:223298/90‑1 (MQ=255)
|
TTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGTATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCAGACCTTTG > NZ_CP009273/674360‑674530
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TAATGTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGTATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCC > NZ_CP009273/674351‑674519
|
TAATGTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAG < SRR3722091.172034/100‑1 (MQ=60)
TTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCAT < SRR3722091.403352/100‑1 (MQ=60)
TTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCC > SRR3722091.2687/1‑100 (MQ=60)
CATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAG > SRR3722091.393839/1‑100 (MQ=60)
GGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGC > SRR3722091.127810/1‑100 (MQ=60)
CATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTACACCAGAGAATTGCTTTACG > SRR3722091.134383/1‑100 (MQ=60)
TTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGG < SRR3722091.270031/100‑1 (MQ=60)
AGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTT > SRR3722091.292091/1‑100 (MQ=60)
TTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCC > SRR3722091.246090/1‑100 (MQ=60)
|
TAATGTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGTATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCC > NZ_CP009273/674351‑674519
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
