BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524762.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 = 1,448,550 number of mapped reads = 1,322,491 (91.3%) number of supplementary alignments = 4,406 (0.3%) number of secondary alignments = 0 number of mapped bases = 76,019,163 bp number of sequenced bases = 75,995,165 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,687 duplication rate = 2.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5022 >>>>>>> ACTG content number of A's = 18,876,422 bp (24.84%) number of C's = 13,517,183 bp (17.79%) number of T's = 23,855,844 bp (31.39%) number of G's = 19,735,563 bp (25.97%) number of N's = 10,153 bp (0.01%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 382,437 number of insertions = 5,368 mapped reads with insertion percentage = 0.4% number of deletions = 14,997 mapped reads with deletion percentage = 1.13% homopolymer indels = 41.56% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.2186X There is a 2.22% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6106280 0.02449855481001991 0.2725644340500885 chr2 243199373 6366416 0.02617776485797108 0.3437468767919452 chr3 198022430 4942587 0.024959733096902203 0.17395855203776409 chr4 191154276 4819943 0.025214936860737554 0.19050693097098345 chr5 180915260 4473655 0.02472790299723749 0.1708884969077505 chr6 171115067 4287368 0.025055467500123763 0.1859481188489439 chr7 159138663 4190131 0.02633006285845194 0.27197033369015255 chr8 146364022 3786805 0.025872512576895434 0.20331036370945274 chr9 141213431 3260313 0.023087839286335305 0.1907468843428623 chr10 135534747 3740287 0.027596517371298153 0.24983547300604314 chr11 135006516 3396129 0.025155296948778383 0.20168298904133364 chr12 133851895 3434611 0.02565978613900087 0.1765422898850553 chr13 115169878 2317150 0.02011941004226817 0.15417273545931445 chr14 107349540 2296873 0.02139620719380819 0.1629378587114093 chr15 102531392 2252493 0.02196881321966252 0.16518478211697918 chr16 90354753 2328984 0.025775998745743902 0.18852012886770264 chr17 81195210 2211917 0.02724196415034828 0.1852854432038975 chr18 78077248 1966682 0.02518892571623426 0.2847210708864405 chr19 59128983 1711047 0.02893753474501667 0.23820454363657068 chr20 63025520 1653083 0.026228787957640016 0.18128428710889527 chr21 48129895 1016358 0.02111697937425378 0.17132853621721206 chr22 51304566 990834 0.01931278397326273 0.1524378979883594 chrMT 16571 25408 1.5332810331301672 1.4924533802336115 chrX 155270560 4180439 0.02692357778576956 0.19163100209027448 chrY 59373566 263370 0.004435812395031149 0.12009397969374389