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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
728,467 |
T→C |
I1143I (ATT→ATC) |
rhsC → |
rhs element protein RhsC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 728,467 | 0 | T | C | 100.0%
| 118.4
/ NA
| 35 | I1143I (ATT→ATC) | rhsC | rhs element protein RhsC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (20/15); total (20/15) |
AAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAAT > NZ_CP009273/728379‑728546
|
aaaGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCa < 2:73226/91‑1 (MQ=37)
aGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCAcc < 1:511637/91‑1 (MQ=255)
gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc < 1:204804/91‑1 (MQ=37)
gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc < 2:464858/91‑1 (MQ=37)
gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc > 2:738964/1‑91 (MQ=255)
gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc > 1:486016/1‑91 (MQ=255)
gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc > 2:755148/1‑91 (MQ=255)
gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc < 1:349742/91‑1 (MQ=37)
gTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATcgc > 2:794710/1‑91 (MQ=255)
gCCTAACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCt < 2:324651/91‑1 (MQ=255)
ccTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCACCTCGGCCTg < 1:809173/91‑1 (MQ=255)
cGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCt < 2:721348/91‑1 (MQ=37)
gTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTgg < 1:45025/91‑1 (MQ=37)
ggCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGcc > 2:783864/1‑91 (MQ=255)
gcgcAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGccc < 2:380859/91‑1 (MQ=25)
gATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATc > 1:353310/1‑91 (MQ=21)
aaaGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAACCCTCCTGTCCCACTGCGCCCATCGCCGCCTGCCGCTGGCCCTTATCAGCAc < 2:441641/91‑1 (MQ=11)
aGCCAGATGGCCCCGGTATACACGCCGGCGCGAAAAATCCCCCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACgg < 2:586258/91‑1 (MQ=255)
ccAGATGGACCGGGTATACACGCCGGCGCGAAAAATCCGCCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGaa < 2:348459/91‑1 (MQ=255)
ccAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGaa < 1:413722/91‑1 (MQ=21)
cAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAg > 2:698161/1‑91 (MQ=21)
cccGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGacaaca > 2:226772/1‑91 (MQ=18)
cccGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGacaaca > 1:828823/1‑91 (MQ=18)
cGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGc < 2:408760/91‑1 (MQ=255)
cGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGc < 1:348857/91‑1 (MQ=255)
gCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCa > 2:780384/1‑91 (MQ=255)
gCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGCCCTGCCCCTCCCCCTTACCAGCACGGAAGGGCCAACAGCGTGGTAcccc > 2:615409/1‑88 (MQ=11)
ccGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAg > 1:626675/1‑91 (MQ=255)
ccGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAg > 1:489718/1‑91 (MQ=255)
cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGa > 1:331789/1‑91 (MQ=255)
cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGa > 2:775519/1‑91 (MQ=255)
cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGa > 1:649259/1‑91 (MQ=255)
cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGa > 2:148855/1‑91 (MQ=255)
cGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGa > 2:382663/1‑91 (MQ=255)
gcgcGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAAt > 2:513838/1‑91 (MQ=255)
gcgcGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAAt > 1:867985/1‑91 (MQ=255)
|
AAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAAT > NZ_CP009273/728379‑728546
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGAT > NZ_CP009273/728368‑728551
|
GGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCC > SRR3722118.772669/1‑101 (MQ=33)
GGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACC < SRR3722118.775834/101‑1 (MQ=24)
AGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTG < SRR3722118.522497/101‑1 (MQ=24)
GGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGC > SRR3722118.496295/1‑101 (MQ=24)
GTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGC < SRR3722118.208894/101‑1 (MQ=24)
GTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGC < SRR3722118.356994/101‑1 (MQ=24)
CCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCACCTCGGCCTGCCGCTGGCCC < SRR3722118.826954/101‑1 (MQ=27)
CGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATC > SRR3722118.360644/1‑101 (MQ=29)
GTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAG < SRR3722118.45839/101‑1 (MQ=24)
ATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGC > SRR3722118.316803/1‑101 (MQ=24)
GCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACA > SRR3722118.847082/1‑101 (MQ=12)
CCAGATGGACCCGGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAG < SRR3722118.422426/101‑1 (MQ=9)
GGTATACAGGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAG > SRR3722118.640136/1‑101 (MQ=38)
GGTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAG > SRR3722118.500092/1‑101 (MQ=39)
GTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGA > SRR3722118.663279/1‑101 (MQ=39)
GTATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGA > SRR3722118.338623/1‑101 (MQ=39)
ATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGctgtctctta > SRR3722118.328446/1‑91 (MQ=12)
ATACACGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAAT > SRR3722118.887320/1‑101 (MQ=39)
CGCCGGCGCGAAAAATCCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGAT < SRR3722118.356084/101‑1 (MQ=37)
|
GGTGAGTGAGGAAAGCCGCCGCTGGCTGGCATCGTGCGGCCTGACGGTGGCGCAGATGCAAAGCCAGATGGACCCGGTATACACGCCGGCGCGAAAAATTCACCTGTACCACTGCGACCATCGCGGCCTGCCGCTGGCCCTTATCAGCACGGAAGGGACAACAGCGTGGTACGCAGAATACGAT > NZ_CP009273/728368‑728551
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
