BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716950.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 = 2,612,873 number of mapped reads = 2,405,709 (92.07%) number of supplementary alignments = 13,086 (0.5%) number of secondary alignments = 0 number of mapped bases = 140,005,456 bp number of sequenced bases = 139,967,163 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,262 duplication rate = 3.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3155 >>>>>>> ACTG content number of A's = 34,712,427 bp (24.8%) number of C's = 29,217,236 bp (20.87%) number of T's = 41,930,882 bp (29.96%) number of G's = 34,104,720 bp (24.37%) number of N's = 1,898 bp (0%) GC percentage = 45.24% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 694,540 number of insertions = 9,600 mapped reads with insertion percentage = 0.4% number of deletions = 24,438 mapped reads with deletion percentage = 1.01% homopolymer indels = 42.01% >>>>>>> Coverage mean coverageData = 0.0452X std coverageData = 0.3602X There is a 3.86% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 17077007 0.06851339800673957 0.5773210246072946 chr2 243199373 12221617 0.05025348893477616 0.4960232117638152 chr3 198022430 9897926 0.049983862939163 0.2597214156408602 chr4 191154276 6571566 0.03437833637579732 0.2319193294797263 chr5 180915260 6191477 0.03422307769947101 0.21443442843720045 chr6 171115067 10616267 0.062041684499939444 0.3802695073596854 chr7 159138663 8158075 0.05126394080613836 0.4735757047339694 chr8 146364022 10000504 0.06832624481991893 0.3393578009757598 chr9 141213431 5964417 0.042236896007434306 0.33606437120639027 chr10 135534747 7309431 0.05393031057932325 0.40501394778866406 chr11 135006516 4762237 0.03527412706509662 0.2984377945782378 chr12 133851895 6410048 0.04788910907835858 0.25979969152928906 chr13 115169878 3247170 0.02819461178903046 0.19145806709165608 chr14 107349540 3163138 0.029465780663801632 0.2484486009886786 chr15 102531392 4235182 0.041306198203180544 0.2358272207701868 chr16 90354753 3149819 0.03486057894486193 0.25171131949060555 chr17 81195210 3441878 0.042390160700366435 0.2502106355293358 chr18 78077248 2791418 0.035752002939447865 0.570107950729621 chr19 59128983 2637357 0.044603456142650044 0.4334618767913775 chr20 63025520 2484567 0.03942160255083972 0.23138891901122488 chr21 48129895 1334503 0.02772711222411767 0.2197448767914174 chr22 51304566 1802484 0.03513301330723663 0.2171693606663911 chrMT 16571 254685 15.369319896204212 9.245907163979247 chrX 155270560 5970147 0.03844996115168259 0.2727187319714909 chrY 59373566 312536 0.005263891341813628 0.12381276443322187