BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173850.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,793,108 number of mapped reads = 6,642,407 (97.78%) number of supplementary alignments = 638,055 (9.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,323,163 number of mapped paired reads (second in pair) = 3,319,244 number of mapped paired reads (both in pair) = 6,540,896 number of mapped paired reads (singletons) = 101,511 number of mapped bases = 786,716,342 bp number of sequenced bases = 786,262,702 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,106,500 duplication rate = 65.7% >>>>>>> Insert size mean insert size = 761,586.9569 std insert size = 8,297,151.751 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.9621 >>>>>>> ACTG content number of A's = 233,027,717 bp (29.64%) number of C's = 157,542,752 bp (20.04%) number of T's = 232,606,386 bp (29.58%) number of G's = 163,076,164 bp (20.74%) number of N's = 9,683 bp (0%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 7,388,388 number of insertions = 77,707 mapped reads with insertion percentage = 1.13% number of deletions = 184,690 mapped reads with deletion percentage = 2.71% homopolymer indels = 42.77% >>>>>>> Coverage mean coverageData = 0.2541X std coverageData = 3.506X There is a 5.33% of reference with a coverageData >= 1X There is a 4.23% of reference with a coverageData >= 2X There is a 3.25% of reference with a coverageData >= 3X There is a 2.67% of reference with a coverageData >= 4X There is a 2.01% of reference with a coverageData >= 5X There is a 1.63% of reference with a coverageData >= 6X There is a 1.2% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.72% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 63205657 0.25358274633947653 2.043111344612372 chr2 243199373 71725344 0.2949240498247502 11.037312917056013 chr3 198022430 65215625 0.32933453548671227 1.665732849270271 chr4 191154276 34504021 0.18050352689991617 1.3773742294243645 chr5 180915260 46257225 0.25568448454818016 1.438665271297315 chr6 171115067 40509763 0.236739895032154 1.5319661096648363 chr7 159138663 41907495 0.26333949406122636 2.0097070385038798 chr8 146364022 43688972 0.29849529551736426 1.8083220446288022 chr9 141213431 35138753 0.24883435485679828 1.6172615428606287 chr10 135534747 34880534 0.25735492021097733 2.5877891968846463 chr11 135006516 29951658 0.22185342520800996 1.3578997240858317 chr12 133851895 38146798 0.28499258826331897 1.532786236505528 chr13 115169878 13763258 0.1195039730787941 0.9846050031342887 chr14 107349540 25154101 0.23431959745705477 1.3865012218208579 chr15 102531392 28400582 0.2769940156474224 1.5143671887274086 chr16 90354753 28495561 0.31537423382696866 1.9097495721786977 chr17 81195210 31013529 0.38196254434220933 2.0167366765854347 chr18 78077248 14865170 0.1903905475766769 1.9750361515482795 chr19 59128983 14697051 0.2485591710582947 1.6310816783705449 chr20 63025520 39227680 0.6224094620718719 2.68160136423678 chr21 48129895 10177476 0.211458512427671 1.3635036214662404 chr22 51304566 7361023 0.14347695680731418 1.0372515052334035 chrMT 16571 1376144 83.04532013758977 76.08319586035837 chrX 155270560 25987087 0.16736647951807476 1.1600449395546533 chrY 59373566 1065835 0.01795133881633453 0.6101260289963449