BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237845.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 = 2,255,593 number of mapped reads = 1,399,953 (62.07%) number of supplementary alignments = 7,041 (0.31%) number of secondary alignments = 0 number of mapped bases = 84,616,865 bp number of sequenced bases = 84,565,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 159,905 duplication rate = 9.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1602 >>>>>>> ACTG content number of A's = 23,085,754 bp (27.3%) number of C's = 16,872,580 bp (19.95%) number of T's = 25,248,776 bp (29.86%) number of G's = 19,284,703 bp (22.8%) number of N's = 74,091 bp (0.09%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 825,516 number of insertions = 6,577 mapped reads with insertion percentage = 0.47% number of deletions = 31,731 mapped reads with deletion percentage = 2.24% homopolymer indels = 46.97% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.2988X There is a 1.6% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 7433676 0.02982410222360088 0.3809193328689464 chr2 243199373 7071445 0.029076740259523615 0.33423882177038594 chr3 198022430 5508727 0.027818702154094363 0.26583680499602014 chr4 191154276 5212256 0.027267273895562764 0.2718046316352333 chr5 180915260 4999127 0.02763242304712162 0.2638801647696273 chr6 171115067 4919638 0.028750466491650323 0.28534889947510256 chr7 159138663 4842339 0.030428425806241693 0.3778791897455374 chr8 146364022 4246704 0.02901467137873541 0.29958550798309175 chr9 141213431 3714901 0.0263069948353567 0.2905699213156661 chr10 135534747 3799927 0.028036552132273504 0.301374279252358 chr11 135006516 3571312 0.02645288617032381 0.2975238177733823 chr12 133851895 4158255 0.03106608987493229 0.28667432514927743 chr13 115169878 2942480 0.02554904156449658 0.26179951990768463 chr14 107349540 2298512 0.021411475074788397 0.23643823931291708 chr15 102531392 2842512 0.027723333747385386 0.27423301710695586 chr16 90354753 2607636 0.028859975966067885 0.2889564742917318 chr17 81195210 2111340 0.026003258073967663 0.2673048067557796 chr18 78077248 2103842 0.02694564746954196 0.37932979816205065 chr19 59128983 1592929 0.02693990187519376 0.3074779589903289 chr20 63025520 1758573 0.027902554393839193 0.2746466226760179 chr21 48129895 1070914 0.02225049524832747 0.24573775885358856 chr22 51304566 933603 0.01819726922551104 0.21607590640582972 chrMT 16571 79065 4.771287188461771 4.667255807762002 chrX 155270560 4527314 0.029157581450083004 0.2785679015845169 chrY 59373566 269838 0.004544749762882694 0.11456395799128767