BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716775.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 = 3,014,608 number of mapped reads = 2,800,937 (92.91%) number of supplementary alignments = 66,127 (2.19%) number of secondary alignments = 0 number of mapped bases = 214,192,254 bp number of sequenced bases = 214,109,367 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 174,594 duplication rate = 4.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.859 >>>>>>> ACTG content number of A's = 53,761,979 bp (25.11%) number of C's = 41,603,249 bp (19.43%) number of T's = 64,109,384 bp (29.94%) number of G's = 54,626,032 bp (25.51%) number of N's = 8,723 bp (0%) GC percentage = 44.94% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,411,641 number of insertions = 18,642 mapped reads with insertion percentage = 0.65% number of deletions = 39,758 mapped reads with deletion percentage = 1.4% homopolymer indels = 39.24% >>>>>>> Coverage mean coverageData = 0.0692X std coverageData = 0.522X There is a 5.33% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 23153935 0.09289419182630643 0.9755696391061849 chr2 243199373 19849074 0.08161646864114243 0.5669045890154268 chr3 198022430 13796356 0.06967067316566108 0.3336640576620342 chr4 191154276 10464274 0.054742557786151745 0.4588397045036679 chr5 180915260 10968858 0.06062981088494138 0.31068941002286843 chr6 171115067 11994203 0.07009437105851117 0.3606324996048682 chr7 159138663 13242017 0.08321055832924774 0.7423344286300505 chr8 146364022 13248202 0.09051542735003551 0.541512511746716 chr9 141213431 6428306 0.04552191639618189 0.3671014532127262 chr10 135534747 11552744 0.08523824521545018 0.7512727963361114 chr11 135006516 8988176 0.06657586808624852 0.43942478754201225 chr12 133851895 8287845 0.06191802514263993 0.31383357330534506 chr13 115169878 3973436 0.03450065302665337 0.22735353424128976 chr14 107349540 4027709 0.03751957390781553 0.26684145171500473 chr15 102531392 4438590 0.04329005891190866 0.25529602448197813 chr16 90354753 6555904 0.07255737835949815 0.36911951146014804 chr17 81195210 5520976 0.06799632638427809 0.3752286180218558 chr18 78077248 5899054 0.07555407178285792 0.5647314029219787 chr19 59128983 5395759 0.0912540471057992 0.7057223188743799 chr20 63025520 5635839 0.08942153908448514 0.4101066426425607 chr21 48129895 3179857 0.06606823056647017 0.41779922557491567 chr22 51304566 3399596 0.06626303007806361 0.34143767587808294 chrMT 16571 36470 2.2008327801581076 2.151024255174614 chrX 155270560 13441286 0.08656686753754221 0.40368576615121654 chrY 59373566 713788 0.012021982981450028 0.4274526256439698