BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524758.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 = 1,528,145 number of mapped reads = 1,386,911 (90.76%) number of supplementary alignments = 4,415 (0.29%) number of secondary alignments = 0 number of mapped bases = 79,219,060 bp number of sequenced bases = 79,194,179 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,415 duplication rate = 2.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4829 >>>>>>> ACTG content number of A's = 18,921,915 bp (23.89%) number of C's = 14,743,396 bp (18.62%) number of T's = 25,452,450 bp (32.14%) number of G's = 20,067,031 bp (25.34%) number of N's = 9,387 bp (0.01%) GC percentage = 43.96% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 400,786 number of insertions = 5,530 mapped reads with insertion percentage = 0.4% number of deletions = 15,079 mapped reads with deletion percentage = 1.08% homopolymer indels = 42.6% >>>>>>> Coverage mean coverageData = 0.0256X std coverageData = 0.2246X There is a 2.29% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6322976 0.025367944820486526 0.2729024047050585 chr2 243199373 6682356 0.027476863601946868 0.3447692229409518 chr3 198022430 5202397 0.0262717561843878 0.17917387440421026 chr4 191154276 5124536 0.026808377543173556 0.20974460230421285 chr5 180915260 4653532 0.025722164067309743 0.17515457851544178 chr6 171115067 4429310 0.025884979491607247 0.18973718131577114 chr7 159138663 4348036 0.02732231073224487 0.26558716970176244 chr8 146364022 3936318 0.026894027276730615 0.20241170951820403 chr9 141213431 3366605 0.023840543892740627 0.19952756147853515 chr10 135534747 3909635 0.02884599769828766 0.28962833757414486 chr11 135006516 3567123 0.026421858038318684 0.20509654422158172 chr12 133851895 3573670 0.026698688128397437 0.18025130714948762 chr13 115169878 2423423 0.021042159999509594 0.15933163763332736 chr14 107349540 2390342 0.022266904916406722 0.1670772189586273 chr15 102531392 2316794 0.022595947980497525 0.16617519133620098 chr16 90354753 2451270 0.027129397387650432 0.20415304747775195 chr17 81195210 2335822 0.028767977815440098 0.19309537503660976 chr18 78077248 2059570 0.026378619287401112 0.29404503789865866 chr19 59128983 1767849 0.02989818038980985 0.2392495420434194 chr20 63025520 1712965 0.02717891101890155 0.1897537659680602 chr21 48129895 1040865 0.021626163946545072 0.18440523587943988 chr22 51304566 1009579 0.019678151063591495 0.15462405424876455 chrMT 16571 25050 1.5116770261299861 1.4465854330902332 chrX 155270560 4294486 0.02765808276855574 0.19406705462067375 chrY 59373566 274551 0.004624128522110328 0.1406777132564261