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 |
|
A3 F1 I1 R1
|
781 |
46.9 |
2231650 |
93.5% |
2086592 |
109.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
723,528 |
(T)8→9 |
coding (887/2685 nt) |
kdpD ← |
fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 723,520 | 1 | . | T | 93.9%
| 144.7
/ 2.6
| 49 | coding (895/2685 nt) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base T (19/27); total (21/28) |
| Fisher's exact test for biased strand distribution p-value = 5.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
CCGAGAATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCG > NC_000913/723387‑723644
|
ccGAGAATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑ttttt > 2:693351/1‑139 (MQ=255)
ccGAGAATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑ttttt > 2:297299/1‑139 (MQ=255)
gaATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑tttttt‑ttt < 1:693351/139‑2 (MQ=255)
ttGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg < 2:413933/139‑1 (MQ=255)
ttGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg < 1:969137/139‑1 (MQ=255)
ttGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg < 1:794490/139‑1 (MQ=255)
aTTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGt < 1:1078525/128‑1 (MQ=255)
aTTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGt > 2:1078525/1‑128 (MQ=255)
cACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAgggg < 2:485557/139‑1 (MQ=255)
cGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGtt < 2:94695/139‑1 (MQ=255)
cGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TTTTTT‑TTCCGGTAAGCGGTg < 1:977476/125‑1 (MQ=255)
cGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TTTTTT‑TTCCGGTAAGCGGTg > 2:977476/1‑125 (MQ=255)
cTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGTCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTT‑TTCCGGTAAGCGGTgc < 2:731620/115‑1 (MQ=255)
cTACCGCTTTCTCTTCCGATGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTTTTTT‑TTCCGGTAAGCGGTgc > 1:731620/1‑115 (MQ=255)
cGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTg < 1:297299/139‑1 (MQ=255)
ttCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAg > 1:826801/1‑139 (MQ=255)
tctcTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTgcagggcagg < 2:1057327/113‑1 (MQ=255)
tctcTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTgcagggcagg > 1:1057327/1‑113 (MQ=255)
tctcTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGtt > 1:567479/1‑117 (MQ=255)
tctcTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGtt < 2:567479/117‑1 (MQ=255)
ttCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg < 2:766229/95‑1 (MQ=255)
ttCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg > 1:766229/1‑95 (MQ=255)
gATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGcc > 2:504665/1‑139 (MQ=255)
gAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGAc > 1:341315/1‑139 (MQ=255)
aaGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTgcagggca < 1:1049751/92‑1 (MQ=255)
aaGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTgcagggca > 2:1049751/1‑92 (MQ=255)
aaGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGc > 1:523204/1‑139 (MQ=255)
tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg > 1:135212/1‑77 (MQ=255)
tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg < 2:135212/77‑1 (MQ=255)
tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg > 2:293506/1‑77 (MQ=255)
tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg < 1:293506/77‑1 (MQ=255)
tGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTgcagggca > 2:442667/1‑86 (MQ=255)
tGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTgcagggca < 1:442667/86‑1 (MQ=255)
tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TTTTTTGTTGCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGACAGCCGCGCCACt > 2:735264/1‑139 (MQ=255)
aGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTgcagggca < 2:226107/70‑1 (MQ=255)
aGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTgcagggca > 1:226107/1‑70 (MQ=255)
aGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg > 1:844491/1‑46 (MQ=39)
aGACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg < 2:844491/46‑1 (MQ=39)
gACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg > 1:739901/1‑45 (MQ=38)
gACGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAg < 2:739901/45‑1 (MQ=38)
aCGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGcc < 1:125010/139‑1 (MQ=255)
aCGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGcc < 2:826801/139‑1 (MQ=255)
cGTAAGGCGCTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCg < 1:400579/139‑1 (MQ=255)
cTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGtt > 2:321216/1‑52 (MQ=255)
cTGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGtt < 1:321216/52‑1 (MQ=255)
tGAGAATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGc < 1:694976/139‑1 (MQ=255)
gagaATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgcc > 1:958680/1‑96 (MQ=255)
gagaATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgcc < 2:958680/96‑1 (MQ=255)
agaATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCg < 2:341315/139‑1 (MQ=255)
agaATTGCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCg < 1:504665/139‑1 (MQ=255)
gCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACa > 2:1024569/1‑49 (MQ=255)
gCCCGACGT‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACa < 1:1024569/49‑1 (MQ=255)
|
CCGAGAATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TTTTTT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCG > NC_000913/723387‑723644
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
