BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124895.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,443,626 number of mapped reads = 4,371,881 (98.39%) number of supplementary alignments = 21,924 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,190,430 number of mapped paired reads (second in pair) = 2,181,451 number of mapped paired reads (both in pair) = 4,351,324 number of mapped paired reads (singletons) = 20,557 number of mapped bases = 381,217,718 bp number of sequenced bases = 381,005,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 333,618 duplication rate = 4.71% >>>>>>> Insert size mean insert size = 38,888.5389 std insert size = 1,864,027.0912 median insert size = 190 >>>>>>> Mapping quality mean mapping quality = 52.7823 >>>>>>> ACTG content number of A's = 106,893,259 bp (28.06%) number of C's = 71,974,217 bp (18.89%) number of T's = 112,407,916 bp (29.5%) number of G's = 89,718,928 bp (23.55%) number of N's = 11,428 bp (0%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 2,794,486 number of insertions = 55,351 mapped reads with insertion percentage = 1.23% number of deletions = 118,561 mapped reads with deletion percentage = 2.66% homopolymer indels = 46.13% >>>>>>> Coverage mean coverageData = 0.1231X std coverageData = 1.349X There is a 8.82% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 29987612 0.12031108239445469 1.171758255701021 chr2 243199373 37166705 0.15282401653231237 1.6520401735889512 chr3 198022430 29204067 0.1474785810880111 0.49235182955748624 chr4 191154276 23311240 0.12194987466563395 0.9700728038797104 chr5 180915260 16645965 0.09200973428112146 0.4297578764563435 chr6 171115067 26241990 0.15335873374610548 2.962623887308874 chr7 159138663 19429272 0.12209020506851939 1.0076192545810534 chr8 146364022 24192273 0.16528838624016495 0.6212720944583662 chr9 141213431 21386297 0.15144662124950423 1.4665957316686862 chr10 135534747 17904574 0.1321032015502268 2.787008848865771 chr11 135006516 14528968 0.10761679088141198 1.22009772941535 chr12 133851895 17856895 0.13340786097948035 0.515876272563642 chr13 115169878 8180027 0.07102575032683459 0.32498684919651577 chr14 107349540 8337535 0.0776671702552242 0.4258488062657184 chr15 102531392 13786370 0.134459990555868 0.47364133462581925 chr16 90354753 12690687 0.14045400577875522 2.2158159990730497 chr17 81195210 7605643 0.09367107985803597 0.8443819044032699 chr18 78077248 7006212 0.08973436153897228 1.4772395987651952 chr19 59128983 4306796 0.07283730890483944 0.8288271370450075 chr20 63025520 10415704 0.16526169081984568 0.5792489834376996 chr21 48129895 5684012 0.11809732807437041 0.6812809620569527 chr22 51304566 6629474 0.12921801151187987 0.4874055235421063 chrMT 16571 122824 7.4119847927101565 4.419041491006458 chrX 155270560 16744951 0.10784369554666384 0.6083318970766136 chrY 59373566 1851625 0.031186016349430655 1.6858320423485096