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 |
|
A6 F1 I2 R1
|
67 |
27.9 |
1239648 |
95.3% |
1181384 |
112.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,071,480 |
C→T |
noncoding (164/195 nt) |
isrC → |
novel sRNA, CP4‑44, putative prophage remnant |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,071,480 | 0 | C | T | 76.9%
| 67.2
/ 20.4
| 39 | noncoding (164/195 nt) | isrC | novel sRNA, CP4‑44, putative prophage remnant |
| Reads supporting (aligned to +/- strand): ref base C (4/5); new base T (16/14); total (20/19) |
| Fisher's exact test for biased strand distribution p-value = 7.16e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
GATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCG > NC_000913/2071349‑2071611
|
gatcgatAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATcc > 1:112645/1‑139 (MQ=255)
gatcgatAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATcc < 2:407458/139‑1 (MQ=255)
atcgatAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCa > 1:30699/1‑139 (MQ=255)
atcgatAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCa > 1:52623/1‑139 (MQ=255)
tcgatAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCa > 2:528379/1‑138 (MQ=255)
tcgatAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCa < 1:528379/138‑1 (MQ=255)
cgatAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACg > 2:233352/1‑139 (MQ=255)
tAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGttt > 2:203673/1‑139 (MQ=255)
aCCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCt > 1:153348/1‑139 (MQ=255)
tGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTAcc < 2:50191/130‑1 (MQ=255)
tGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTAcc > 1:50191/1‑130 (MQ=255)
tGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCtttttt > 1:220617/1‑139 (MQ=255)
cAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTAtt < 2:153348/139‑1 (MQ=255)
cATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCt < 1:203673/139‑1 (MQ=255)
cATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCt < 2:52623/139‑1 (MQ=255)
cATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCt < 2:220617/139‑1 (MQ=255)
acaGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATc > 2:421247/1‑139 (MQ=255)
cAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGc < 2:228703/139‑1 (MQ=255)
aGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCt < 1:262322/118‑1 (MQ=255)
aGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCt > 2:262322/1‑118 (MQ=255)
cAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGAc < 1:532683/139‑1 (MQ=255)
aGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACa > 1:274512/1‑139 (MQ=255)
aacaGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAAt < 1:233352/139‑1 (MQ=255)
ccACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGa < 1:342854/130‑1 (MQ=255)
ccACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGa > 2:342854/1‑130 (MQ=255)
ttCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGc < 2:274512/139‑1 (MQ=255)
cTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATgg < 2:112645/139‑1 (MQ=255)
ccACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAAt < 2:30699/139‑1 (MQ=255)
ggACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCt > 2:569168/1‑71 (MQ=255)
ggACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCt < 1:569168/71‑1 (MQ=255)
ccGGCACTGTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGgcgc > 1:221665/1‑139 (MQ=255)
gTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCt < 2:272575/107‑1 (MQ=255)
gTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCt > 1:272575/1‑107 (MQ=255)
gTAACCCTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTgg > 2:349055/1‑139 (MQ=255)
tAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGt < 1:128400/139‑1 (MQ=255)
cccTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCtgatga > 1:602583/1‑75 (MQ=255)
cccTTTACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCtgatga < 2:602583/75‑1 (MQ=255)
tACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCg > 2:157082/1‑139 (MQ=255)
tACCTGCTGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCg > 2:547627/1‑139 (MQ=255)
|
GATCGATAAGCTAATAATAACCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCG > NC_000913/2071349‑2071611
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
