BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472755.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 3,933,142 number of mapped reads = 3,674,719 (93.43%) number of supplementary alignments = 126,840 (3.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,928,409 number of mapped paired reads (second in pair) = 1,746,310 number of mapped paired reads (both in pair) = 3,468,000 number of mapped paired reads (singletons) = 206,719 number of mapped bases = 329,985,730 bp number of sequenced bases = 329,911,019 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,899,388 duplication rate = 34.16% >>>>>>> Insert size mean insert size = 1,302,748.7469 std insert size = 11,298,155.1424 median insert size = 297 >>>>>>> Mapping quality mean mapping quality = 45.6564 >>>>>>> ACTG content number of A's = 85,599,749 bp (25.95%) number of C's = 63,131,174 bp (19.14%) number of T's = 117,932,502 bp (35.75%) number of G's = 63,200,992 bp (19.16%) number of N's = 46,602 bp (0.01%) GC percentage = 38.29% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 3,327,378 number of insertions = 61,068 mapped reads with insertion percentage = 1.63% number of deletions = 30,248 mapped reads with deletion percentage = 0.81% homopolymer indels = 39.59% >>>>>>> Coverage mean coverageData = 0.1066X std coverageData = 11.0661X There is a 2.03% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.15% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.06% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 35149836 0.1410220598808458 3.5955468667390402 chr2 243199373 26356902 0.10837569881399324 6.266221503888194 chr3 198022430 32667350 0.16496792812814184 3.8020980314845754 chr4 191154276 11151387 0.05833710463269993 5.296796315593499 chr5 180915260 15940443 0.0881099969123666 5.243877995073786 chr6 171115067 24507076 0.1432198603527999 21.07549097756532 chr7 159138663 17814217 0.11194147710038257 15.726911577255494 chr8 146364022 13551072 0.0925847200345451 3.4861753302052887 chr9 141213431 17193159 0.12175300095923595 3.087819993590618 chr10 135534747 10118028 0.07465264977400961 3.7852241936005937 chr11 135006516 15517743 0.11494069664015329 4.28523648523113 chr12 133851895 17082542 0.12762271314873802 32.33290479797822 chr13 115169878 5629383 0.048878952533057296 1.485293585516134 chr14 107349540 7086934 0.06601736719132657 1.9374750930398474 chr15 102531392 9608006 0.09370794458735135 22.190300411097567 chr16 90354753 11866456 0.1313318403958229 6.631212671550248 chr17 81195210 10981447 0.1352474733423314 2.8333275464540333 chr18 78077248 5693214 0.07291770837004911 5.5692056622700985 chr19 59128983 6391374 0.10809206713398065 2.2013301684013196 chr20 63025520 6075840 0.09640285395503281 3.9690141523190006 chr21 48129895 2589820 0.05380896841765393 4.862479288582696 chr22 51304566 2383828 0.04646424647661965 0.9095558091771779 chrMT 16571 5437430 328.12926196367147 1000.2406290305227 chrX 155270560 17289639 0.11135168830459553 3.6931254297124205 chrY 59373566 1902604 0.032044630770535154 12.409253452149807