BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716204.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 = 2,701,185 number of mapped reads = 2,457,114 (90.96%) number of supplementary alignments = 62,024 (2.3%) number of secondary alignments = 0 number of mapped bases = 181,165,949 bp number of sequenced bases = 181,103,189 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,363 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8552 >>>>>>> ACTG content number of A's = 47,463,712 bp (26.21%) number of C's = 37,743,637 bp (20.84%) number of T's = 53,442,797 bp (29.51%) number of G's = 42,431,611 bp (23.43%) number of N's = 21,432 bp (0.01%) GC percentage = 44.27% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,291,936 number of insertions = 15,190 mapped reads with insertion percentage = 0.61% number of deletions = 36,776 mapped reads with deletion percentage = 1.47% homopolymer indels = 40.4% >>>>>>> Coverage mean coverageData = 0.0585X std coverageData = 0.4527X There is a 4.87% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 14819332 0.05945554695328121 0.5498403264728832 chr2 243199373 15867963 0.06524672660237492 0.6699655774562148 chr3 198022430 12251085 0.061867158180010214 0.2887251117986519 chr4 191154276 11843275 0.06195663130235182 0.32158345961005347 chr5 180915260 11214156 0.061985683241977486 0.29360988078538724 chr6 171115067 10659462 0.06229411697568397 0.338690096165013 chr7 159138663 10208830 0.06415053267099523 0.5545102337582315 chr8 146364022 9472399 0.06471808351918616 0.5976766209830215 chr9 141213431 7973225 0.05646222844057942 0.49971940970349243 chr10 135534747 8825175 0.06511374533351215 0.4668887183980426 chr11 135006516 8323235 0.06165061692281579 0.48534045210394555 chr12 133851895 8410665 0.06283560647385679 0.2981385255471029 chr13 115169878 5853122 0.05082163931787789 0.26012407473972937 chr14 107349540 5639905 0.0525377658814374 0.3471900178316472 chr15 102531392 5397512 0.052642531177183274 0.2683811856088704 chr16 90354753 5616909 0.06216506396735986 0.33576603335606525 chr17 81195210 5112151 0.06296123872331878 0.325139974322579 chr18 78077248 5216463 0.06681156333788814 0.969949606127339 chr19 59128983 3737522 0.06320964458326639 0.5172559773716487 chr20 63025520 4015245 0.06370824072534427 0.3134799206366326 chr21 48129895 2473221 0.05138637846602408 0.29583205788367484 chr22 51304566 2177329 0.042439283084472444 0.23979906155708436 chrMT 16571 14739 0.889445416691811 1.3209252219218666 chrX 155270560 5636204 0.03629924436416021 0.3185089873492836 chrY 59373566 406825 0.006851954959215352 0.22468674468940217