BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716166.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 = 2,349,833 number of mapped reads = 2,092,569 (89.05%) number of supplementary alignments = 10,612 (0.45%) number of secondary alignments = 0 number of mapped bases = 118,536,702 bp number of sequenced bases = 118,505,486 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,515 duplication rate = 3.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2812 >>>>>>> ACTG content number of A's = 30,980,842 bp (26.14%) number of C's = 22,496,387 bp (18.98%) number of T's = 37,230,285 bp (31.42%) number of G's = 27,796,263 bp (23.46%) number of N's = 1,709 bp (0%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 638,300 number of insertions = 8,358 mapped reads with insertion percentage = 0.4% number of deletions = 18,643 mapped reads with deletion percentage = 0.88% homopolymer indels = 39.9% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.3129X There is a 3.36% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% 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 8771715 0.035192349631096805 0.47523994126324803 chr2 243199373 9703189 0.03989808394777399 0.3667066137411303 chr3 198022430 6722278 0.03394705337168118 0.2027595787015822 chr4 191154276 7516428 0.03932126530091328 0.25065783865431573 chr5 180915260 6596898 0.036464021885163254 0.2127127584131875 chr6 171115067 6360933 0.03717342436011202 0.2374452133881581 chr7 159138663 7199812 0.045242380853733825 0.3489240968612373 chr8 146364022 5201457 0.035537811334536845 0.2980419049126786 chr9 141213431 5682246 0.04023870788891178 0.3584880657536814 chr10 135534747 4619050 0.03408019052118052 0.34698261399020963 chr11 135006516 4708951 0.03487943500445564 0.2808015478000378 chr12 133851895 9043204 0.06756126986472623 0.3247410508324243 chr13 115169878 4595066 0.03989815809303888 0.21837341309917982 chr14 107349540 4386709 0.04086378944893476 0.2651966704994211 chr15 102531392 3053315 0.029779318708557084 0.18972238724677193 chr16 90354753 2776563 0.03072957324115534 0.22042331378924168 chr17 81195210 3624409 0.04463821203245857 0.24143119988378026 chr18 78077248 2993202 0.038336417799971635 0.6049159088514341 chr19 59128983 1998633 0.03380124092443802 0.3652689489034879 chr20 63025520 3556470 0.05642904651956858 0.27459864008670337 chr21 48129895 1454454 0.03021934703992186 0.2275109058497719 chr22 51304566 1205607 0.02349901956094902 0.1673979853382547 chrMT 16571 14417 0.8700138796693018 1.1685923099973208 chrX 155270560 6415652 0.04131917860024463 0.27740463917781205 chrY 59373566 336044 0.005659825114765719 0.14086368233889163