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 |
|
A29 F119 I0 R1
|
76 |
56.4 |
2152892 |
90.0% |
1937602 |
142.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,196,232 |
C→T |
100% |
T370T (ACC→ACT) |
icd → |
isocitrate dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,196,232 | 0 | C | T | 100.0%
| 87.0
/ ‑6.7
| 35 | T370T (ACC→ACT) | icd | isocitrate dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (13/21); minor base G (1/0); total (14/21) |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGAT > NC_000913/1196092‑1196312
|
ccTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTATATGGAAAGAGTGTG‑TGAGATGATGCTGCGCCATCTGGGTTGGACTGa > 2:220922/1‑143 (MQ=255)
cTGGTGCAAACAGCGGTGACGAATGCGCCCTGCTTGAAGCCACCCACGGGACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGaa < 2:85240/143‑1 (MQ=255)
cAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCt > 2:254530/1‑143 (MQ=255)
ggTAACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGAcctgat < 2:619867/143‑6 (MQ=38)
cggttGCGTCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTa < 2:395629/139‑1 (MQ=38)
cGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACCAAGTACATCCTGGCTCTAT‑TGTTCGCTCCGTTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTa < 2:676700/143‑1 (MQ=37)
aaTGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTATAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTaaa < 2:500941/143‑1 (MQ=38)
aTGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAg > 1:751269/1‑143 (MQ=255)
ggcgcCCTGTTTAAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAgg < 1:1069071/142‑1 (MQ=37)
cccTGTTTGAAGGCACCCTCGGTACTGCGCCGAAATCTGCCGGTCAGGACACAGTAAAGCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATg < 1:908850/143‑1 (MQ=25)
tggttGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGaa < 1:7862/140‑1 (MQ=37)
tGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGACGCGGCTGACCTGATTGTTACAGGTATGGaa > 1:37862/1‑143 (MQ=37)
tGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGGAAATCCTGGCTCTAT‑TATTCTCTCCGCGGAGATGATGCTGCGCCATATGGGTTGGGCTGAAGCGGCTGAGCTGACGGTTAAAGGGATGGaa > 2:28130/1‑143 (MQ=37)
gAAGCCACCCACGGTACTGCGCCGAACTATGGCCGTCAGCACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGATATGATACTTCGCCATATGGATTCGACGGAGGCGCCGGACCTCAATCTTAAAGGTATGGAAGgcgc > 2:523169/1‑143 (MQ=255)
aGCCACCCGTGGCACTGCCCCTAAAGATGCCGGTCAGGACAAAGTAAATCCTGGGTCTAG‑TACTTTCTCCGCTGAGATTATTCTGTGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCaa < 2:166237/143‑1 (MQ=17)
aGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCAGAGATAATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCaa < 1:673933/143‑1 (MQ=25)
cccacGGTACTGCGCCGAAATATGCCAGTCAGAACAAATTAAGTCCTGGCTCTAT‑TATTCGCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaat < 1:443585/143‑2 (MQ=18)
gcacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatg < 1:1036081/142‑3 (MQ=25)
cacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgc < 1:71016/143‑1 (MQ=21)
ggTACCGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatgccaa < 1:542731/143‑7 (MQ=21)
gTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaag > 1:525706/1‑142 (MQ=21)
gTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTGAAAGGTATGGGAGGCGCAATCAATGCCaag > 2:137970/1‑142 (MQ=21)
gTACCGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatgccaag < 1:937945/143‑8 (MQ=18)
aCTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGAc < 2:906732/143‑1 (MQ=18)
cTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCCGATTGTTACAGGGATGGAAGGCGCAATCAATGCCAAGAcc > 2:838275/1‑143 (MQ=21)
gcgcCGAAATATACCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGt < 1:883611/143‑1 (MQ=18)
cGAAATATGCCGGTCAGGACAAAGTAAATCCGGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAAct > 2:938155/1‑142 (MQ=17)
gCCTGTCAGCACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGTACTGAAGCGGCTGACCTTATTTTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACtt < 1:632423/143‑1 (MQ=17)
gCCGGTCAGGACAAAGTAGATCCGGGCTCTAT‑TATTCTCTCCGCTGGGATGATGCTGCTCCATATGGGTTGGAGTGAAGCGGCTGACCTGAGTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACtt < 2:269061/143‑1 (MQ=14)
ccGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTCTGACTTc > 1:464001/1‑143 (MQ=17)
cGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg > 1:998018/1‑143 (MQ=14)
gTCAGGATAAAGCAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGaa < 1:753236/143‑2 (MQ=11)
gACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCt > 2:581987/1‑143 (MQ=14)
gACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCt > 2:232251/1‑143 (MQ=14)
aaaGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgat < 1:808122/143‑1 (MQ=11)
|
CCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAT‑TATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGAT > NC_000913/1196092‑1196312
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
