BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524488.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 = 879,536 number of mapped reads = 816,355 (92.82%) number of supplementary alignments = 1,946 (0.22%) number of secondary alignments = 0 number of mapped bases = 47,631,398 bp number of sequenced bases = 47,616,456 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,899 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3862 >>>>>>> ACTG content number of A's = 11,408,482 bp (23.96%) number of C's = 8,479,930 bp (17.81%) number of T's = 15,574,595 bp (32.71%) number of G's = 12,152,611 bp (25.52%) number of N's = 838 bp (0%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 219,177 number of insertions = 2,513 mapped reads with insertion percentage = 0.31% number of deletions = 8,625 mapped reads with deletion percentage = 1.05% homopolymer indels = 46.12% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 0.1637X There is a 1.42% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4692690 0.018827194817701176 0.2558575165437057 chr2 243199373 3742000 0.015386552826351242 0.1794216824157796 chr3 198022430 2658756 0.01342653960967957 0.12379667137726173 chr4 191154276 2741303 0.014340788275120772 0.13764753215428768 chr5 180915260 2560072 0.014150669213862889 0.1267877267597446 chr6 171115067 2018495 0.01179612663798916 0.12845530634211377 chr7 159138663 2334034 0.014666668401003218 0.19538735752634573 chr8 146364022 4328861 0.02957599101779261 0.19584660724905859 chr9 141213431 2074044 0.014687299822068624 0.1553519091154115 chr10 135534747 2484272 0.01832941039097524 0.1763594313838199 chr11 135006516 1628814 0.01206470656571865 0.1548611826069064 chr12 133851895 2196675 0.01641123571690935 0.13638900189686695 chr13 115169878 1072282 0.00931043792544436 0.10460935275164891 chr14 107349540 1126818 0.010496719408392434 0.1101962231343604 chr15 102531392 1265837 0.012345848186670479 0.12074558580570977 chr16 90354753 1526064 0.01688969256548131 0.14407163937663708 chr17 81195210 1679791 0.020688301686762063 0.1572260062726102 chr18 78077248 1124545 0.014402979469768196 0.23105514576322017 chr19 59128983 965150 0.016322790466394458 0.19919784700939508 chr20 63025520 1368151 0.021707889121739894 0.15877875084263998 chr21 48129895 655946 0.013628660523776336 0.12939511772277457 chr22 51304566 397916 0.007755956847973336 0.093844290791507 chrMT 16571 2223 0.1341500211212359 0.36641193953664564 chrX 155270560 2840526 0.018294041059683176 0.1532391470180531 chrY 59373566 146133 0.0024612468114177275 0.07481928551627758