BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818901.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,710,911 number of mapped reads = 1,678,476 (98.1%) number of supplementary alignments = 23,531 (1.38%) number of secondary alignments = 0 number of mapped bases = 155,568,502 bp number of sequenced bases = 155,475,986 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 250,298 duplication rate = 11.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3213 >>>>>>> ACTG content number of A's = 44,214,212 bp (28.44%) number of C's = 33,180,948 bp (21.34%) number of T's = 44,249,802 bp (28.46%) number of G's = 33,828,515 bp (21.76%) number of N's = 2,509 bp (0%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 929,336 number of insertions = 22,239 mapped reads with insertion percentage = 1.29% number of deletions = 45,657 mapped reads with deletion percentage = 2.65% homopolymer indels = 39.96% >>>>>>> Coverage mean coverageData = 0.0503X std coverageData = 0.6722X There is a 3.84% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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% 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 15129679 0.06070066722120624 1.0245145927243196 chr2 243199373 11716567 0.04817679772554348 0.8402709040484126 chr3 198022430 9417898 0.047559753710728625 0.27190588796043297 chr4 191154276 7479778 0.03912953534976115 0.3721152217728327 chr5 180915260 6657834 0.036800842560212994 0.24932522088961345 chr6 171115067 7379241 0.04312443742899624 0.28788378624209676 chr7 159138663 13686312 0.08600243172836007 1.5631194062596516 chr8 146364022 12915276 0.08824078365378618 0.5433691898771399 chr9 141213431 5762144 0.04080450392852504 0.6203317422830766 chr10 135534747 7554158 0.055735950870222234 1.0693912761062911 chr11 135006516 6858357 0.050800192488487 0.37929189743596053 chr12 133851895 5996472 0.04479930597919439 0.261170363974478 chr13 115169878 4446484 0.03860804645464676 0.238097705159903 chr14 107349540 4487290 0.04180073803762922 0.2804668245532856 chr15 102531392 4397235 0.04288671902552537 0.25490954249580583 chr16 90354753 4156717 0.04600440886601726 0.5704573305634814 chr17 81195210 4435775 0.05463099362634816 0.4540397660408418 chr18 78077248 2903851 0.03719202551811252 0.6473252659040447 chr19 59128983 3009413 0.050895734161367195 0.8940870545447337 chr20 63025520 7143770 0.11334725996707365 0.46443765830421735 chr21 48129895 1512105 0.03141716806155509 0.30841551316080407 chr22 51304566 1557440 0.030356752262556904 0.22963830347932987 chrMT 16571 363793 21.953593627421398 14.395867071501408 chrX 155270560 5976286 0.03848949858878592 0.3212305510624771 chrY 59373566 624627 0.01052028776577105 0.7335243769204015