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 |
|
A2 F5 I177 R1
|
141 |
27.5 |
996908 |
97.7% |
973979 |
124.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
415,362 |
T→C |
S106P (TCC→CCC) |
brnQ → |
branched‑chain amino acid transporter carrier protein BrnQ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 415,362 | 0 | T | C | 100.0%
| 28.2
/ NA
| 9 | S106P (TCC→CCC) | brnQ | branched‑chain amino acid transporter carrier protein BrnQ |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (4/5); total (4/5) |
CCAATCGGTAAAGTCGCTGGCGTACTGCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTTCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTACAGCCTGGTCTATTTCGC > NZ_CP009273/415272‑415438
|
ccAATCGGTAAAGTCGCTGGCGTACTGCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGc < 1:161440/139‑1 (MQ=255)
ccAATCGGTAAAGTCGCTGGCGTACTGCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGc > 2:413633/1‑139 (MQ=255)
aaGTCGCTGGCGTACTGCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTa < 1:413633/139‑1 (MQ=255)
tttGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTACAGCCTGGTCTATTTCGc > 1:1092/1‑130 (MQ=255)
tttGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTACAGCCTGGTCTATTTCGc < 2:1092/130‑1 (MQ=255)
gggCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGc > 1:178466/1‑85 (MQ=255)
gggCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGc < 2:178466/85‑1 (MQ=255)
cGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGc > 1:473651/1‑74 (MQ=255)
cGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGc < 2:473651/74‑1 (MQ=255)
|
CCAATCGGTAAAGTCGCTGGCGTACTGCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTTCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTACAGCCTGGTCTATTTCGC > NZ_CP009273/415272‑415438
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCGGTATTAACGGTAGTGGCGCTGGCAAAAGTTGGCGGCGGTGTTGACAGCCTCAGCACGCCAATCGGTAAAGTCGCTGGCGTACTGCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTTCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTACAGCCTGGTCTATTTCGCTATCGTTATTCTGGTTTCGCTCTATCCGGGCAAGCTGC > NZ_CP009273/415212‑415476
|
CCGGTATTAACGGTAGTGGCGCTGGCAAAAGTTGGCGGCGGTGTTGACAGCCTCAGCACGCCAATCGGTAAAGTCGCTGGCGTACTGCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTC < SRR3722131.448700/151‑1 (MQ=60)
GCCAATCGGTAAAGTCGCTGGCGTACTGCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTAC < SRR3722131.163300/151‑1 (MQ=60)
tttgtttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagCAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTAC < SRR3722131.181336/71‑1 (MQ=60)
AAAGTCGCTGGCGTACTGCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTACAGCCTGGTCT < SRR3722131.418113/151‑1 (MQ=60)
GCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTACAGCCTGGTCTATTTCGCTATCGTTATT > SRR3722131.1100/1‑151 (MQ=60)
ACCTGGCGGCGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTACctgtctcttatacacatctccgagcccacgagaccgtact > SRR3722131.180507/1‑107 (MQ=60)
GGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTCCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTACctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccg > SRR3722131.478733/1‑96 (MQ=60)
|
CCGGTATTAACGGTAGTGGCGCTGGCAAAAGTTGGCGGCGGTGTTGACAGCCTCAGCACGCCAATCGGTAAAGTCGCTGGCGTACTGCTGGCAACGGTTTGTTACCTGGCGGTGGGGCCGCTTTTCGCTACGCCGCGTACAGCTACCGTTTCCTTTGAAGTGGGGATTGCGCCGCTGACGGGTGATTCCGCGCTGCCGCTGTTTATCTACAGCCTGGTCTATTTCGCTATCGTTATTCTGGTTTCGCTCTATCCGGGCAAGCTGC > NZ_CP009273/415212‑415476
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
