BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524699.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 = 1,755,890 number of mapped reads = 1,624,786 (92.53%) number of supplementary alignments = 6,753 (0.38%) number of secondary alignments = 0 number of mapped bases = 96,644,199 bp number of sequenced bases = 96,614,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,457 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0211 >>>>>>> ACTG content number of A's = 25,454,166 bp (26.35%) number of C's = 18,136,491 bp (18.77%) number of T's = 30,839,075 bp (31.92%) number of G's = 22,172,166 bp (22.95%) number of N's = 12,768 bp (0.01%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 479,041 number of insertions = 7,709 mapped reads with insertion percentage = 0.47% number of deletions = 18,574 mapped reads with deletion percentage = 1.13% homopolymer indels = 42.99% >>>>>>> Coverage mean coverageData = 0.0312X std coverageData = 0.3022X There is a 2.79% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 7777610 0.031203974412565255 0.5485853622201975 chr2 243199373 8199949 0.033716982485806 0.40626170567470227 chr3 198022430 6424633 0.0324439660699043 0.19676164787221195 chr4 191154276 6238694 0.032636957595445056 0.22947982876087908 chr5 180915260 5851758 0.032345298014108924 0.19751672864514672 chr6 171115067 5647885 0.03300635706147373 0.2243182858209237 chr7 159138663 5319462 0.03342658471373484 0.36251179938527006 chr8 146364022 4911924 0.03355964077018873 0.3467908023743464 chr9 141213431 4026478 0.028513420936567994 0.24786336362304304 chr10 135534747 4684985 0.034566670936420456 0.3190542658391226 chr11 135006516 4444324 0.03291932961220924 0.25309365186104055 chr12 133851895 4274212 0.03193239811808417 0.19680600786108907 chr13 115169878 3010848 0.026142669005866273 0.17766043983707042 chr14 107349540 2906575 0.02707580302626355 0.18645617168235862 chr15 102531392 2765374 0.02697099830654791 0.1800404749538946 chr16 90354753 2784616 0.030818699709134284 0.20692059654779593 chr17 81195210 2606695 0.03210404899500845 0.20672107443047927 chr18 78077248 2572416 0.03294706288828213 0.44504432369453095 chr19 59128983 1969274 0.03330471623366159 0.3970394164287823 chr20 63025520 2036884 0.032318400546318383 0.19798902720144848 chr21 48129895 1274095 0.0264720087172432 0.20997818501754373 chr22 51304566 1145816 0.022333606720306338 0.16348285834430007 chrMT 16571 32583 1.966266368957818 1.8239783074241787 chrX 155270560 5409712 0.034840551872808344 0.2248303988927918 chrY 59373566 327397 0.0055141879131868216 0.20338996277689722