BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231722.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 836,426 number of mapped reads = 356,094 (42.57%) number of supplementary alignments = 1,597 (0.19%) number of secondary alignments = 0 number of mapped bases = 22,040,707 bp number of sequenced bases = 22,025,369 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,403 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6342 >>>>>>> ACTG content number of A's = 6,075,022 bp (27.58%) number of C's = 3,766,579 bp (17.1%) number of T's = 7,135,751 bp (32.4%) number of G's = 5,047,569 bp (22.92%) number of N's = 448 bp (0%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 257,249 number of insertions = 1,847 mapped reads with insertion percentage = 0.51% number of deletions = 8,804 mapped reads with deletion percentage = 2.44% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.0071X std coverageData = 0.1041X There is a 0.66% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 1905618 0.007645389176382433 0.12502124210183313 chr2 243199373 1610694 0.006622936482652856 0.1059461906636206 chr3 198022430 1874255 0.009464862137082147 0.10340196174144788 chr4 191154276 1123599 0.005877969478433221 0.08279918290814495 chr5 180915260 1298225 0.00717587338956371 0.09219852344483757 chr6 171115067 1499066 0.00876057279047204 0.10489626112308477 chr7 159138663 1331163 0.008364799445374252 0.12383713668959066 chr8 146364022 1171611 0.008004774561333113 0.16959481245201066 chr9 141213431 887811 0.006287015291059673 0.09259573919569955 chr10 135534747 1060064 0.007821344883611286 0.0990117967982805 chr11 135006516 1024229 0.007586515305676061 0.11009014068163936 chr12 133851895 844235 0.006307232333169433 0.08439277563063234 chr13 115169878 830368 0.007209940779827864 0.09094132464535665 chr14 107349540 882893 0.008224469336338098 0.09813124703596605 chr15 102531392 513051 0.005003843115677197 0.07600753360733949 chr16 90354753 568890 0.006296182338077998 0.08495104693959547 chr17 81195210 544439 0.006705309340292364 0.09024595455905927 chr18 78077248 507866 0.0065046606150872535 0.12633136214677496 chr19 59128983 494241 0.008358692724344675 0.1088251066569031 chr20 63025520 479600 0.007609615914315344 0.09327618536775723 chr21 48129895 335154 0.006963530670490763 0.0888994936209236 chr22 51304566 214615 0.004183155939765673 0.06876776556918557 chrMT 16571 13468 0.8127451572023414 1.1842400834287592 chrX 155270560 945005 0.0060861827251734 0.08471276147039676 chrY 59373566 80547 0.0013566138169972812 0.04062465181927366