BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716121.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 = 1,431,792 number of mapped reads = 1,215,416 (84.89%) number of supplementary alignments = 4,839 (0.34%) number of secondary alignments = 0 number of mapped bases = 68,420,810 bp number of sequenced bases = 68,400,970 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,865 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0691 >>>>>>> ACTG content number of A's = 17,239,159 bp (25.2%) number of C's = 13,666,585 bp (19.98%) number of T's = 21,074,152 bp (30.81%) number of G's = 16,420,022 bp (24.01%) number of N's = 1,052 bp (0%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 351,169 number of insertions = 5,490 mapped reads with insertion percentage = 0.45% number of deletions = 12,495 mapped reads with deletion percentage = 1.02% homopolymer indels = 38.67% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.2255X There is a 2.02% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 5553849 0.022282187212685017 0.24789101643736175 chr2 243199373 6520874 0.02681287340325503 0.2906404476156319 chr3 198022430 5092109 0.02571480917591002 0.1821540329530557 chr4 191154276 3678655 0.01924442956222439 0.1523809600750589 chr5 180915260 3366966 0.018610735213823313 0.14604256609633356 chr6 171115067 3697653 0.021609160811069898 0.17037817671677397 chr7 159138663 4201818 0.02640350195728363 0.5253497352747751 chr8 146364022 5486048 0.037482216770457426 0.23457573788674355 chr9 141213431 2796848 0.019805821444845426 0.16478590948886213 chr10 135534747 3206416 0.023657520089663795 0.265531717823068 chr11 135006516 2423048 0.017947637431070362 0.16315489397394684 chr12 133851895 3144244 0.02349047056823514 0.16981697531037387 chr13 115169878 1704490 0.01479978992423696 0.12947638177135395 chr14 107349540 2160719 0.020127883174906946 0.15435249052738373 chr15 102531392 1608210 0.015685049901595017 0.13839535874400416 chr16 90354753 2100962 0.023252368361850316 0.16929074906615624 chr17 81195210 2885734 0.03554069260982267 0.2103115590154663 chr18 78077248 1561680 0.020001729569156947 0.23112724454310332 chr19 59128983 1447853 0.02448635045862365 0.23639137092444096 chr20 63025520 1456695 0.023112780346754774 0.16767742252909237 chr21 48129895 665064 0.013818106189510699 0.12815628434943033 chr22 51304566 1033153 0.020137642329924398 0.15319261999378161 chrMT 16571 117535 7.092812745157202 4.74431818696966 chrX 155270560 2365995 0.015237885404676842 0.14823991900689049 chrY 59373566 144192 0.002428555495555042 0.0661566127517265