BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716486.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 = 708,587 number of mapped reads = 533,638 (75.31%) number of supplementary alignments = 3,190 (0.45%) number of secondary alignments = 0 number of mapped bases = 30,559,709 bp number of sequenced bases = 30,550,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,479 duplication rate = 1.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5444 >>>>>>> ACTG content number of A's = 7,988,880 bp (26.15%) number of C's = 5,937,489 bp (19.43%) number of T's = 9,571,669 bp (31.33%) number of G's = 7,052,376 bp (23.08%) number of N's = 380 bp (0%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 154,690 number of insertions = 2,196 mapped reads with insertion percentage = 0.41% number of deletions = 5,653 mapped reads with deletion percentage = 1.05% homopolymer indels = 39.02% >>>>>>> Coverage mean coverageData = 0.0099X std coverageData = 0.1202X There is a 0.94% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2455173 0.009850218186617878 0.18156951093212134 chr2 243199373 2604139 0.010707835994297567 0.13580441193409298 chr3 198022430 2024861 0.010225412343440083 0.1050951057088678 chr4 191154276 1972971 0.010321354255240412 0.10928698647211148 chr5 180915260 1846707 0.010207580057094134 0.10524020678506915 chr6 171115067 1754047 0.010250687042070937 0.11153447616264706 chr7 159138663 1661605 0.01044124016550271 0.1340748680284034 chr8 146364022 1540188 0.010522995876677944 0.12117137811606958 chr9 141213431 1267333 0.008974592508838624 0.10625114809183953 chr10 135534747 1470812 0.010851918290739128 0.11961078294883988 chr11 135006516 1391373 0.010305969231885074 0.11444901804190727 chr12 133851895 1379859 0.010308849194850771 0.10606621178267908 chr13 115169878 953013 0.0082748459627612 0.09426874230344365 chr14 107349540 947599 0.008827229255011247 0.09958493693836758 chr15 102531392 872218 0.008506838569011138 0.09750457427914758 chr16 90354753 890260 0.009852940442435829 0.105022115112825 chr17 81195210 847053 0.010432302595190037 0.10781031647161719 chr18 78077248 814620 0.010433513230384349 0.1453853577479593 chr19 59128983 635373 0.010745542503242446 0.14117999151943272 chr20 63025520 637724 0.010118504377274476 0.10513250028542258 chr21 48129895 408510 0.008487656164635307 0.09839646549962781 chr22 51304566 361571 0.007047540369019007 0.08684564718722561 chrMT 16571 6427 0.3878462374026915 0.6850148063841047 chrX 155270560 1722066 0.011090743795861882 0.1134986196998093 chrY 59373566 94207 0.0015866825314147376 0.05368929328133193