BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524485.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 = 3,051,999 number of mapped reads = 2,824,332 (92.54%) number of supplementary alignments = 7,038 (0.23%) number of secondary alignments = 0 number of mapped bases = 165,810,995 bp number of sequenced bases = 165,756,434 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,749 duplication rate = 4.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4804 >>>>>>> ACTG content number of A's = 40,282,877 bp (24.3%) number of C's = 32,252,332 bp (19.46%) number of T's = 54,335,840 bp (32.78%) number of G's = 38,882,093 bp (23.46%) number of N's = 3,292 bp (0%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 764,970 number of insertions = 11,398 mapped reads with insertion percentage = 0.4% number of deletions = 32,017 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.23% >>>>>>> Coverage mean coverageData = 0.0536X std coverageData = 0.4481X There is a 4.46% of reference with a coverageData >= 1X There is a 0.63% 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 16295460 0.06537781103462126 0.8848253342592486 chr2 243199373 13067781 0.05373279066800884 0.4905108295408794 chr3 198022430 9202614 0.04647258393910225 0.2573233696352709 chr4 191154276 9506372 0.04973141171061222 0.315336187747664 chr5 180915260 9212901 0.050923846888316665 0.265181764543334 chr6 171115067 7149300 0.041780657456657516 0.3320681780797092 chr7 159138663 8318445 0.052271678316161294 0.5886614493453783 chr8 146364022 15111007 0.10324263294705033 0.46113009460213156 chr9 141213431 7051193 0.04993287784360965 0.38476839907996735 chr10 135534747 8787781 0.0648378456042715 0.48751549465399524 chr11 135006516 5708271 0.04228144810432705 0.4028418696187459 chr12 133851895 7838412 0.058560336407639205 0.28424087524785185 chr13 115169878 3758565 0.032634965541944914 0.21086692013717448 chr14 107349540 3750719 0.03493931133752413 0.23166850267081754 chr15 102531392 4364071 0.04256326686757554 0.25364844099965766 chr16 90354753 5081210 0.05623622257038321 0.3092956388440683 chr17 81195210 5716155 0.07040015045222495 0.3361637397699501 chr18 78077248 3920275 0.0502102097655901 0.704390838825855 chr19 59128983 3312389 0.05601971879002215 0.6330392358293597 chr20 63025520 4735356 0.07513394574134415 0.32973274648395196 chr21 48129895 2276652 0.04730224323157156 0.28762912675788505 chr22 51304566 1333333 0.025988583550243853 0.18863653787891235 chrMT 16571 31708 1.9134632792227386 1.986224372869466 chrX 155270560 9769163 0.06291703333845128 0.3418381599466119 chrY 59373566 511862 0.008621041895984486 0.21637404024798118