BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054600.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,294,024 number of mapped reads = 6,069,883 (73.18%) number of supplementary alignments = 178 (0%) number of secondary alignments = 0 number of mapped bases = 285,781,359 bp number of sequenced bases = 285,722,926 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,256,559 duplication rate = 15.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6205 >>>>>>> ACTG content number of A's = 87,366,201 bp (30.58%) number of C's = 53,840,713 bp (18.84%) number of T's = 87,062,088 bp (30.47%) number of G's = 57,179,546 bp (20.01%) number of N's = 274,378 bp (0.1%) GC percentage = 38.86% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,920,893 number of insertions = 12,670 mapped reads with insertion percentage = 0.21% number of deletions = 40,012 mapped reads with deletion percentage = 0.66% homopolymer indels = 47.01% >>>>>>> Coverage mean coverageData = 0.0923X std coverageData = 0.7138X There is a 4.52% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 25347344 0.10169420600962113 0.7832936513754786 chr2 243199373 23974689 0.09858038984335704 0.7801698643940319 chr3 198022430 21919075 0.1106898597295266 0.7531444543630081 chr4 191154276 17251255 0.0902478111449623 0.6789040216858833 chr5 180915260 13405913 0.07410050981879583 0.5629562826505877 chr6 171115067 14609804 0.08537999754282304 0.6961891852183366 chr7 159138663 18672773 0.11733649540589643 0.883646799789995 chr8 146364022 15282746 0.10441600190516766 0.7780114765334536 chr9 141213431 13826135 0.09790948992663452 0.735742387969133 chr10 135534747 12046201 0.08887906065888772 0.6808244560061321 chr11 135006516 12643442 0.09365060572335634 0.6895894854156162 chr12 133851895 10324247 0.07713187026601305 0.5819477981140249 chr13 115169878 8770942 0.07615656239559444 0.6067061584042586 chr14 107349540 6427521 0.05987469531774426 0.5551827747477934 chr15 102531392 8866603 0.08647695917363533 0.626794960136204 chr16 90354753 7532927 0.08337056712445443 0.7195174362465324 chr17 81195210 5095487 0.06275600494167081 0.5096006470409218 chr18 78077248 11176918 0.1431520485967948 0.9515264387718386 chr19 59128983 4355674 0.0736639424358102 0.6311467021741525 chr20 63025520 5156017 0.08180840078749053 0.6113108736230619 chr21 48129895 3699184 0.0768583434474561 0.6809568888819466 chr22 51304566 2456127 0.047873458280496904 0.4309647930537483 chrMT 16571 22600 1.363828374871764 3.638006200297047 chrX 155270560 22189936 0.1429114186230796 0.9326391003059956 chrY 59373566 727799 0.012257963417592267 0.24878387739959607