BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230372.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 = 3,905,754 number of mapped reads = 3,321,172 (85.03%) number of supplementary alignments = 32,061 (0.82%) number of secondary alignments = 0 number of mapped bases = 233,571,275 bp number of sequenced bases = 233,463,593 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 383,116 duplication rate = 9.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6521 >>>>>>> ACTG content number of A's = 68,703,792 bp (29.43%) number of C's = 46,752,243 bp (20.03%) number of T's = 69,001,321 bp (29.56%) number of G's = 48,878,905 bp (20.94%) number of N's = 127,332 bp (0.05%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 2,015,842 number of insertions = 19,510 mapped reads with insertion percentage = 0.58% number of deletions = 63,704 mapped reads with deletion percentage = 1.9% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.0755X std coverageData = 1.1713X There is a 2.04% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 38970212 0.15634950815227858 1.5141968255035276 chr2 243199373 8939159 0.03675650512470688 0.8246062113265126 chr3 198022430 8026797 0.04053478689257575 0.6310907429300461 chr4 191154276 9673688 0.05060670471216663 0.6421393401720529 chr5 180915260 20914754 0.11560525076767986 1.006127710426607 chr6 171115067 6915289 0.04041309231991827 0.6009981997974434 chr7 159138663 29253478 0.18382382664607405 3.3876025640802157 chr8 146364022 13706936 0.09364962654551813 0.9986200032557194 chr9 141213431 5510003 0.03901897263582527 0.7245205989783324 chr10 135534747 8454965 0.06238226865912105 1.1759215158465763 chr11 135006516 11398346 0.08442811752878654 0.9754362130868413 chr12 133851895 5117044 0.038229148716945695 0.5667310854985247 chr13 115169878 9500839 0.08249413097407293 0.8451832840382683 chr14 107349540 16668986 0.15527766583815822 1.1783439236868392 chr15 102531392 2270092 0.022140458212056655 0.4258707742425178 chr16 90354753 2229450 0.02467440755440945 0.47071032645148125 chr17 81195210 7865376 0.09686995082591694 0.9013590954483843 chr18 78077248 5507314 0.0705367330569848 1.3660224461742634 chr19 59128983 3135220 0.05302340478272728 0.9003012014548704 chr20 63025520 7804760 0.12383491639577111 1.0358755444412466 chr21 48129895 3264826 0.06783364060943826 0.7459408264969529 chr22 51304566 2542447 0.049555959600165025 0.6155433177810945 chrMT 16571 35151 2.1212358940317424 3.7344473331684593 chrX 155270560 5397433 0.03476147055823074 0.5502574188253999 chrY 59373566 468710 0.007894253816589019 0.26934545552335687