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 F17 I0 R1
|
43 |
55.2 |
1410130 |
81.3% |
1146435 |
215.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
2,173,361 |
Δ2 bp |
100% |
pseudogene (1‑2/442 nt) |
gatC ← |
pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,173,361 | 0 | C | . | 75.0%
| 22.0
/ 4.4
| 12 | pseudogene (2/442 nt) | gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| Reads supporting (aligned to +/- strand): ref base C (1/2); new base . (8/1); total (9/3) |
| Fisher's exact test for biased strand distribution p-value = 1.27e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
| * | NC_000913 | 2,173,362 | 0 | C | . | 75.1%
| 22.1
/ 3.3
| 12 | pseudogene (1/442 nt) | gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| Reads supporting (aligned to +/- strand): ref base C (1/1); new base . (8/1); total (9/3) |
| Fisher's exact test for biased strand distribution p-value = 3.45e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
TAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑GCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCG > NC_000913/2173154‑2173574
||
tAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATAAGGCTTGCCGGAACCACCC‑‑CCGTATGTCCcagcagaa > 1:559969/1‑226 (MQ=255)
gATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGCAACCA‑‑CAGCCGTATGTCCCAGCAGAAACGCCGGAACAAAGCCaacccgac > 1:312322/1‑221 (MQ=255)
tGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGGGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATAAAGGCCAATCAGGAACt > 1:380797/1‑228 (MQ=255)
ataTTTCCCCGAAGCCCCGGGACCCGCCAACCCCCAGAAAAGGCAGAGGGGGGAAAAATCACAAAAGGGAAGCACATAAATCCCCGGCACACAAAAAGAAATAAAAATGGTGAGGGGAATAAAAATCGGGCTGCCCGATCCCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGc < 2:548018/226‑1 (MQ=255)
cACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAAATCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGACTGCTTAGCGATgg > 1:162870/1‑227 (MQ=255)
cacacaACGCGCAATAAAAATGGTGAGTGGGATAAAAATCA‑GCCTGGCGGTACC‑CCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGACCTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑g < 1:223575/228‑1 (MQ=255)
cacacaAA‑AACAATTAAAAGGGGTAGGGGGAAAAAAACCCCGCATGGCCACACC‑CACCCCCGTAGCCCCCAGCAGACCCCCCGAAAAAAGGCCAACCAGGACCCCCTGACCGCCGAACTTCCCCTGTAAACGACTACGAGCCTGCTGAGCGATGGGCGTTAAACCATCCATGATGGTTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑g < 2:384834/228‑1 (MQ=255)
cacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑GCt > 1:384834/1‑228 (MQ=255)
gCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGCCTACGAGCCTGCTTAGCGATGGGCGTTAAACACTCCATGATGGGTTTAATCACCCTGGGCATTAGCAGCATCACTGCCGCCGTTTTTTCCGCCA‑CCTGCAATac > 2:186896/1‑227 (MQ=255)
aGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCAGGGCATTAGCAGCAACACTGCCGCCGTTTTTACAGCCA‑CCGGCAAAACACCTTTGACACCGaaa > 2:45319/1‑228 (MQ=255)
gATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTACCGATGGGCGTTAAACCATCCATAAGGGGTTTAATCACCCGTGACATTAGGCCATTCACTGCCACC‑TCTTTTTCGCCACCCTGGAATACCCCTTTGCCATccacaccccc > 2:98517/1‑219 (MQ=255)
aGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGATTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑CCCGCAATCCACCTTTGACATCGTAACCCCCGTGGactccc > 2:110162/1‑223 (MQ=255)
||
TAGTTTGCGTCGCGATCCACAGGGTGATGCTCATAATGATGACACCCGAGATTAAGGTGCGGAACAGATTTCCACGATGCACGGCGA‑CCGCCATCGCCACGAAGAAGCCGATGGTGGCAAGATCGCCAAACGGCAGCACCTGATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTCCTGACCGCCGAACTTCGCCTGTAAACGACTACGAGCCTGCTTAGCGATGGGCGTTAAACCATCCATGATGGGTTTAATCACCCGTGGCATTAGCAGCATCACTGCCGCCGTTTTTACCGCCA‑GCTGCAATACACCTTTGACATCGTAACCCGCGAGGATGCCG > NC_000913/2173154‑2173574
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
