BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525219.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 = 1,301,072 number of mapped reads = 1,190,258 (91.48%) number of supplementary alignments = 3,339 (0.26%) number of secondary alignments = 0 number of mapped bases = 70,581,574 bp number of sequenced bases = 70,558,010 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,344 duplication rate = 1.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2592 >>>>>>> ACTG content number of A's = 17,804,390 bp (25.23%) number of C's = 13,963,799 bp (19.79%) number of T's = 21,678,021 bp (30.72%) number of G's = 17,110,003 bp (24.25%) number of N's = 1,797 bp (0%) GC percentage = 44.04% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 351,655 number of insertions = 4,162 mapped reads with insertion percentage = 0.35% number of deletions = 14,405 mapped reads with deletion percentage = 1.2% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.0228X std coverageData = 0.2377X There is a 2.11% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% 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 7797012 0.03128181574319929 0.43979523927251696 chr2 243199373 5513021 0.02266873031782035 0.27680770973694807 chr3 198022430 5624625 0.028403979286588898 0.18067945934572152 chr4 191154276 3942211 0.02062319024451224 0.15795956375921422 chr5 180915260 3248217 0.017954356089143614 0.14208064874149573 chr6 171115067 4040603 0.023613367722901922 0.18484294619690597 chr7 159138663 4529398 0.028461958361432255 0.4057209693005757 chr8 146364022 3272819 0.02236081623938976 0.1866034182262176 chr9 141213431 2356138 0.01668494266667878 0.16663283646767912 chr10 135534747 3916572 0.028897180145250872 0.2629751820394183 chr11 135006516 3260476 0.02415050840953484 0.19467058283840485 chr12 133851895 3243137 0.02422929462448029 0.16603567873713024 chr13 115169878 2218708 0.019264655294676965 0.14910507192240174 chr14 107349540 2707609 0.025222362387393556 0.17156891644234099 chr15 102531392 1975889 0.019271063831845764 0.14683837846610412 chr16 90354753 1957065 0.02165979027135407 0.17109401070488428 chr17 81195210 1449516 0.01785223537201271 0.14666328955726182 chr18 78077248 1550994 0.019864865114098285 0.31893620380826987 chr19 59128983 1284442 0.021722714222904865 0.2949978257725906 chr20 63025520 1344613 0.021334421358205374 0.15620701279047183 chr21 48129895 924603 0.019210575880126063 0.15157092737419192 chr22 51304566 601521 0.011724512005422676 0.11434426201791585 chrMT 16571 4541 0.2740329491279947 0.5563213776482058 chrX 155270560 3613209 0.02327040618646574 0.1710550425989177 chrY 59373566 204635 0.0034465674505721956 0.10072302861067377