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 |
|
A10 F1 I2 R1
|
757 |
38.1 |
1607544 |
96.5% |
1551279 |
117.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,767,445 |
(C)7→8 |
intergenic (+90/‑265) |
rnlB → / → yfjP |
CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,767,438 | 1 | . | C | 86.1%
| 127.1
/ 12.5
| 43 | intergenic (+83/‑272) | rnlB/yfjP | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
| Reads supporting (aligned to +/- strand): ref base . (6/0); new base C (16/21); total (22/21) |
| Fisher's exact test for biased strand distribution p-value = 2.11e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAA > NC_000913/2767304‑2767567
|
ctctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑c‑cc‑c < 2:722674/139‑1 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑c‑cc‑cc > 2:442012/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑c‑cc‑cc > 1:801038/1‑139 (MQ=255)
cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGt > 2:467384/1‑139 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTc < 1:562807/139‑1 (MQ=255)
ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAac < 2:801038/139‑1 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑‑A‑CA‑TCAC‑TCACCAAGTCCTGCATAGGTAACACGt > 2:314256/1‑139 (MQ=255)
tGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTc > 2:113401/1‑139 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTccc < 2:500254/139‑1 (MQ=255)
cAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTcccc < 1:113401/139‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTccc > 1:159428/1‑134 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTccc < 2:159428/134‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCtgtg > 2:685733/1‑139 (MQ=255)
ttttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 1:442012/139‑1 (MQ=255)
ttttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 1:467384/139‑1 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAccc < 1:685733/139‑1 (MQ=255)
tctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 1:12975/139‑1 (MQ=255)
tctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 1:558137/139‑1 (MQ=255)
ccAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑C‑CCACACC‑ACACAAATTCCCCCATAGCGAACAAGTGTTCCCCTGTGCACCCACTACTAAATTCCCTCCCAATTaaa > 1:53571/1‑139 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑C‑CC‑CCCCACCATGACGTCCTGCCTATGGAACACGTTTTCCCTTGTTGTCACACAACTAAAATTCCTCCCCTTTAACATTCGCaataa > 2:714778/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑‑C‑CC‑CCCC‑TCACAACGCACTGCTTAGGGAACAAGTTTACCTATGTGAACCCACGACTAAATTTCGCCCCCTTCATACAACTAAATACTGt > 2:171808/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAac > 1:113040/1‑80 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAac < 2:113040/80‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CACC‑CCCC‑ACACAACGTCATGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTCAATTTCCCCCCCTTTAAACTTCTCAATAATga > 1:271537/1‑138 (MQ=255)
ttttGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGACCTGCATAGGGAACACGTCTTCCCCTGTGCACCCACGAATACCTTTCCCCCCCTTTAACCTGCTCAATAATGTCAcc < 1:314256/139‑1 (MQ=255)
gATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACCACGTCCTGCATAGGGCACACGTTTTCCCCTGTGCACCCACGCCTAAATTTCCCCCCCTTTAAACTTATCAACAATGTCACCTATTTTCTg > 2:400370/1‑139 (MQ=255)
tGTCCAATATGATCAAATAGCATT‑AA‑‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCTTGTGCACCGGCGACTAAATTTCCCCCCCTTTACACTTCTCAATAATCTCACCAATTTTCTGGAAATCCTacg > 2:540089/1‑137 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCC‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg < 2:447612/129‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCC‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAAAACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg > 1:447612/1‑129 (MQ=255)
tCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTc < 2:527722/42‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTc > 1:527722/1‑42 (MQ=255)
tCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatga > 1:635122/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTat < 2:130633/137‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCACTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTat > 1:130633/1‑137 (MQ=255)
cAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatgatg > 1:233098/1‑139 (MQ=255)
cAATATGATCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatgatg < 1:171808/139‑1 (MQ=255)
aTCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTcc < 1:694141/139‑1 (MQ=255)
tCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGtttt < 1:284861/52‑1 (MQ=255)
tCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTccc < 1:530908/55‑1 (MQ=255)
tCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTccc > 2:530908/1‑55 (MQ=255)
tCAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACCTCCTGCATAGGGAACACGtttt > 2:284861/1‑52 (MQ=255)
cAAATAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg < 2:53571/139‑1 (MQ=255)
aaTAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTc > 2:275956/1‑50 (MQ=255)
aaTAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTc < 1:275956/50‑1 (MQ=255)
tAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGTACCCACGACTAACTTTCCCCCCCTTTAAACTTCTCAATAATTTAACCAATTTTTTGGAAATCCTTTAATGCCTTTCCCGGTaa > 1:697862/1‑139 (MQ=255)
tAGCATT‑AAC‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGATTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaa > 2:414482/1‑139 (MQ=255)
|
CTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑C‑CC‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAA > NC_000913/2767304‑2767567
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
