BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716393.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 = 2,371,990 number of mapped reads = 2,128,648 (89.74%) number of supplementary alignments = 32,630 (1.38%) number of secondary alignments = 0 number of mapped bases = 166,033,436 bp number of sequenced bases = 165,958,980 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,273 duplication rate = 3.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8963 >>>>>>> ACTG content number of A's = 42,026,187 bp (25.32%) number of C's = 31,943,154 bp (19.25%) number of T's = 52,065,651 bp (31.37%) number of G's = 39,914,385 bp (24.05%) number of N's = 9,603 bp (0.01%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,482,936 number of insertions = 15,225 mapped reads with insertion percentage = 0.71% number of deletions = 42,630 mapped reads with deletion percentage = 1.97% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.0536X std coverageData = 0.5897X There is a 4.46% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% 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 13144134 0.052734608833732856 0.8920938982003851 chr2 243199373 14005162 0.05758716326953688 0.9314462854367364 chr3 198022430 10973209 0.055413970023496836 0.2746003825406288 chr4 191154276 10802117 0.05650994173941471 0.3079958931499681 chr5 180915260 9900542 0.054724747928947506 0.2828718609705371 chr6 171115067 9552421 0.055824546414723376 0.3647781779916363 chr7 159138663 9299239 0.05843481919915338 0.7835115701839475 chr8 146364022 8603649 0.058782540151841416 0.79816414185589 chr9 141213431 7151093 0.05064031763380921 0.6620254173767204 chr10 135534747 7820089 0.057698038127447865 0.5385814145473714 chr11 135006516 7461726 0.055269376775858726 0.5716221097924891 chr12 133851895 7646213 0.057124428458782746 0.29076686099496074 chr13 115169878 5210950 0.04524577164178293 0.24418502740280768 chr14 107349540 5009283 0.04666329264196195 0.3851989259800949 chr15 102531392 4717319 0.046008533659623 0.2580722323209363 chr16 90354753 4711154 0.05214063282315652 0.3233776486663348 chr17 81195210 4432573 0.05459155780248613 0.3132251777511505 chr18 78077248 4628622 0.05928259664070127 1.2873201277311972 chr19 59128983 3420289 0.05784454300524668 0.6850739881188835 chr20 63025520 3355547 0.053241083929176626 0.29747382295353997 chr21 48129895 2162560 0.044931741488320305 0.2776407550388344 chr22 51304566 1828995 0.035649750940296425 0.21839599141404226 chrMT 16571 15530 0.9371794098123227 1.2357809492824825 chrX 155270560 9708755 0.06252798341166542 0.4401310606417984 chrY 59373566 472265 0.007954128946878481 0.22531865696824424