BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6230408.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 4,259,042
number of mapped reads = 3,910,296 (91.81%)
number of supplementary alignments = 37,930 (0.89%)
number of secondary alignments = 0
number of mapped bases = 280,202,652 bp
number of sequenced bases = 280,073,660 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 261,715
duplication rate = 4.66%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.516
>>>>>>> ACTG content
number of A's = 83,851,657 bp (29.94%)
number of C's = 56,922,938 bp (20.32%)
number of T's = 81,786,953 bp (29.2%)
number of G's = 57,285,864 bp (20.45%)
number of N's = 226,248 bp (0.08%)
GC percentage = 40.78%
>>>>>>> Mismatches and indels
general error rate = 0.0096
number of mismatches = 2,624,152
number of insertions = 27,008
mapped reads with insertion percentage = 0.69%
number of deletions = 73,794
mapped reads with deletion percentage = 1.86%
homopolymer indels = 46.66%
>>>>>>> Coverage
mean coverageData = 0.0905X
std coverageData = 1.0419X
There is a 3.61% of reference with a coverageData >= 1X
There is a 1.93% of reference with a coverageData >= 2X
There is a 1.2% of reference with a coverageData >= 3X
There is a 0.77% of reference with a coverageData >= 4X
There is a 0.49% of reference with a coverageData >= 5X
There is a 0.31% of reference with a coverageData >= 6X
There is a 0.2% of reference with a coverageData >= 7X
There is a 0.12% of reference with a coverageData >= 8X
There is a 0.08% of reference with a coverageData >= 9X
There is a 0.05% of reference with a coverageData >= 10X
There is a 0.03% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 25460463 0.10214804239143702 1.7492867836681312
chr2 243199373 21210910 0.08721613768305234 1.277292873957666
chr3 198022430 9002319 0.04546110761291031 0.4291137105215387
chr4 191154276 19841998 0.10380096336427232 0.9249398947831382
chr5 180915260 16253399 0.08983984546135025 0.6165056238022579
chr6 171115067 14125669 0.08255070256320561 0.631775524543899
chr7 159138663 17290099 0.10864800969202562 0.9485703709469208
chr8 146364022 18558190 0.126794752879912 1.1935234904644747
chr9 141213431 19493549 0.13804316531336172 1.1467474606775883
chr10 135534747 17534799 0.12937493438490721 1.3121550346695885
chr11 135006516 12987380 0.09619817164972985 0.9705586512073106
chr12 133851895 8676938 0.06482491712201759 0.5440466527481348
chr13 115169878 14574400 0.1265469778478015 0.7297939206023593
chr14 107349540 3287312 0.030622506626483914 0.543365776090823
chr15 102531392 10245507 0.09992556230973632 0.6426894454410725
chr16 90354753 6912369 0.07650254989906287 0.7276192220793124
chr17 81195210 6573789 0.08096276861652307 0.6844927693481944
chr18 78077248 8921297 0.11426244172950357 2.3850374272506585
chr19 59128983 4369372 0.07389560547659005 1.232582270596261
chr20 63025520 5976208 0.09482203399511817 0.7146654883408317
chr21 48129895 4274589 0.08881359496005549 0.8505336842288214
chr22 51304566 3416191 0.06658649056694096 0.5082805081214571
chrMT 16571 18302 1.104459598093054 1.6344863099140774
chrX 155270560 10257977 0.0660651768113672 0.6112799774018021
chrY 59373566 939626 0.015825662214730373 0.7186556551950178