BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716677.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,164,782
number of mapped reads = 2,852,985 (90.15%)
number of supplementary alignments = 11,290 (0.36%)
number of secondary alignments = 0
number of mapped bases = 164,785,925 bp
number of sequenced bases = 164,734,410 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 126,153
duplication rate = 3.29%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.0695
>>>>>>> ACTG content
number of A's = 40,989,281 bp (24.88%)
number of C's = 32,309,410 bp (19.61%)
number of T's = 51,570,582 bp (31.31%)
number of G's = 39,863,857 bp (24.2%)
number of N's = 1,280 bp (0%)
GC percentage = 43.81%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 858,592
number of insertions = 11,506
mapped reads with insertion percentage = 0.4%
number of deletions = 32,383
mapped reads with deletion percentage = 1.13%
homopolymer indels = 41.49%
>>>>>>> Coverage
mean coverageData = 0.0532X
std coverageData = 0.3866X
There is a 4.46% of reference with a coverageData >= 1X
There is a 0.62% of reference with a coverageData >= 2X
There is a 0.12% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% 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 13092003 0.052525457900463965 0.5238682136643881
chr2 243199373 13839287 0.056905109701907 0.5763458114700396
chr3 198022430 10895992 0.0550240293485945 0.2770148582915482
chr4 191154276 10556925 0.05522725005638901 0.32365559300512686
chr5 180915260 9867793 0.05454372947865205 0.27189489051592863
chr6 171115067 9423666 0.055072099524701705 0.32907093949566063
chr7 159138663 9030668 0.05674716520648411 0.4997402345028391
chr8 146364022 8166144 0.055793383431346266 0.3862284685261546
chr9 141213431 6967977 0.049343585455408984 0.32309486948630234
chr10 135534747 7988527 0.058940804309023424 0.5007075979959934
chr11 135006516 7391640 0.05475024627700192 0.34918338793283243
chr12 133851895 7502323 0.056049434339349474 0.2805568343495626
chr13 115169878 5147900 0.04469831946856799 0.246357322591153
chr14 107349540 4923457 0.045863792243543845 0.2689980266948937
chr15 102531392 4843688 0.0472410244854571 0.26419645456838536
chr16 90354753 4950125 0.05478544111564336 0.30851954456515585
chr17 81195210 4708268 0.05798701672179923 0.29974325444536404
chr18 78077248 4306665 0.05515902660913458 0.5794253578220939
chr19 59128983 3684935 0.06232028377690853 0.46322679376028386
chr20 63025520 3555439 0.056412688066675216 0.28953028645444856
chr21 48129895 2170269 0.045091912209656804 0.29143214344851454
chr22 51304566 2010518 0.03918789606367589 0.23272008460293755
chrMT 16571 59256 3.5758855832478424 2.771194372288435
chrX 155270560 9180802 0.059127770261149314 0.31703228702354846
chrY 59373566 521658 0.008786031143893227 0.2649830052699541