BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524744.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 = 2,011,172 number of mapped reads = 1,847,367 (91.86%) number of supplementary alignments = 8,284 (0.41%) number of secondary alignments = 0 number of mapped bases = 107,112,836 bp number of sequenced bases = 107,077,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,075 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9895 >>>>>>> ACTG content number of A's = 27,721,772 bp (25.89%) number of C's = 19,396,254 bp (18.11%) number of T's = 33,261,771 bp (31.06%) number of G's = 26,695,470 bp (24.93%) number of N's = 2,209 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 537,083 number of insertions = 6,683 mapped reads with insertion percentage = 0.36% number of deletions = 22,100 mapped reads with deletion percentage = 1.19% homopolymer indels = 44.09% >>>>>>> Coverage mean coverageData = 0.0346X std coverageData = 0.3405X There is a 3.1% of reference with a coverageData >= 1X There is a 0.26% 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 11522250 0.046227567874344434 0.6747440421814 chr2 243199373 9170862 0.03770923373227611 0.4350551505542346 chr3 198022430 8682367 0.04384537145615272 0.234686899396705 chr4 191154276 6314818 0.033035190905172325 0.2108665134738359 chr5 180915260 4985161 0.0275552266845815 0.18194145204226383 chr6 171115067 5516460 0.03223830663608366 0.23095765614604932 chr7 159138663 6454479 0.04055883641551016 0.5015124685092972 chr8 146364022 5117649 0.03496521160097664 0.31657249929419257 chr9 141213431 3571074 0.025288486900371394 0.23859919117018052 chr10 135534747 5872825 0.04333077037433065 0.3808490421400354 chr11 135006516 4987388 0.036941831755735406 0.27229608475692496 chr12 133851895 4956955 0.03703313277708919 0.21667592869240895 chr13 115169878 3523405 0.030593112202480583 0.19232996186334497 chr14 107349540 4072077 0.03793287796109792 0.21794130096518252 chr15 102531392 2950380 0.02877538227511824 0.18864677381012956 chr16 90354753 2835288 0.03137951137999348 0.2230928810860193 chr17 81195210 2105487 0.025931172540843234 0.1823132560121789 chr18 78077248 2350326 0.03010257226279287 0.4751252307274293 chr19 59128983 1893899 0.032029960670894676 0.467707764730748 chr20 63025520 1978189 0.03138711112577889 0.1976838302667705 chr21 48129895 1407943 0.029252982995288064 0.19966617062607117 chr22 51304566 833863 0.016253192747015928 0.1393607217921268 chrMT 16571 22563 1.3615955585058235 1.3871617571518347 chrX 155270560 5675254 0.036550740848748146 0.23374119040451974 chrY 59373566 311874 0.00525274159884552 0.14917238292183013