BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716582.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 = 787,775 number of mapped reads = 714,525 (90.7%) number of supplementary alignments = 3,778 (0.48%) number of secondary alignments = 0 number of mapped bases = 41,426,024 bp number of sequenced bases = 41,414,318 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,061 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5232 >>>>>>> ACTG content number of A's = 10,482,466 bp (25.31%) number of C's = 8,290,766 bp (20.02%) number of T's = 12,761,235 bp (30.81%) number of G's = 9,879,356 bp (23.85%) number of N's = 495 bp (0%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 203,936 number of insertions = 2,779 mapped reads with insertion percentage = 0.39% number of deletions = 7,506 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.03% >>>>>>> Coverage mean coverageData = 0.0134X std coverageData = 0.1512X There is a 1.25% of reference with a coverageData >= 1X There is a 0.06% 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 3452826 0.013852828073796454 0.20212109765179836 chr2 243199373 3931672 0.016166456152828978 0.19023841569383435 chr3 198022430 2902231 0.014656072041939895 0.12904594507862316 chr4 191154276 2335478 0.012217764880132737 0.12507388609625741 chr5 180915260 2233890 0.012347714615118702 0.11722898437439842 chr6 171115067 2229892 0.013031535089776752 0.12455293341122708 chr7 159138663 1980204 0.012443261509618187 0.20835456494875504 chr8 146364022 3415327 0.023334470816878755 0.1912954368331833 chr9 141213431 1551641 0.01098791374879915 0.11909219967234289 chr10 135534747 1968408 0.014523272028537449 0.18315582914737596 chr11 135006516 1486547 0.011010927798477519 0.12140624144403571 chr12 133851895 1926275 0.014391092483225582 0.1311500189640961 chr13 115169878 1063826 0.009237015949604462 0.10092633796702319 chr14 107349540 1334189 0.012428455678524566 0.11848712736066595 chr15 102531392 982504 0.009582470118029804 0.10239694776180153 chr16 90354753 1300469 0.014392922971080448 0.12866656531452647 chr17 81195210 1800118 0.022170248712947475 0.1597632343016003 chr18 78077248 937080 0.012001959905144197 0.16297791758425942 chr19 59128983 864426 0.014619328054399312 0.17909899491002867 chr20 63025520 971742 0.015418230583420811 0.1334597041662399 chr21 48129895 435058 0.00903924681323323 0.1046306567651424 chr22 51304566 681737 0.013288037559853834 0.1212412902568876 chrMT 16571 129792 7.832478426166194 5.370730282613673 chrX 155270560 1407235 0.009063115377441802 0.10766884644856137 chrY 59373566 103457 0.001742475767751595 0.05952359323776768