BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617389.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,242,246 (94.51%) number of supplementary alignments = 91,831 (0.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,205,925 number of mapped paired reads (second in pair) = 15,036,321 number of mapped paired reads (both in pair) = 29,677,310 number of mapped paired reads (singletons) = 564,936 number of mapped bases = 2,963,024,315 bp number of sequenced bases = 2,962,152,309 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,607,714 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 62,703.8744 std insert size = 2,385,757.1142 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.4113 >>>>>>> ACTG content number of A's = 898,831,506 bp (30.34%) number of C's = 586,927,353 bp (19.81%) number of T's = 886,790,765 bp (29.94%) number of G's = 588,838,059 bp (19.88%) number of N's = 764,626 bp (0.03%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 30,220,693 number of insertions = 299,900 mapped reads with insertion percentage = 0.96% number of deletions = 361,883 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.41% >>>>>>> Coverage mean coverageData = 0.9571X std coverageData = 9.8574X There is a 52.9% of reference with a coverageData >= 1X There is a 23.94% of reference with a coverageData >= 2X There is a 9.23% of reference with a coverageData >= 3X There is a 3.26% of reference with a coverageData >= 4X There is a 1.12% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192261608 0.7713585917204194 19.912070092441922 chr2 243199373 292818702 1.2040273722251742 8.925411561225538 chr3 198022430 236091222 1.1922448482224968 1.523357991916344 chr4 191154276 162677651 0.8510280512898388 9.401176553106119 chr5 180915260 185847511 1.0272627693208412 1.4800183260662505 chr6 171115067 139062189 0.8126823162801906 3.694814072577428 chr7 159138663 240250454 1.5096925503263778 10.971130478258608 chr8 146364022 124735979 0.8522311514505935 7.8123736341760255 chr9 141213431 124774803 0.8835901947598738 14.996204941269589 chr10 135534747 124880254 0.9213892139408354 20.36820666919867 chr11 135006516 158998755 1.177711711336955 5.771224689163569 chr12 133851895 130714587 0.9765613478987354 1.3938525907559178 chr13 115169878 129314834 1.122818190360504 1.3191984767633693 chr14 107349540 85810641 0.7993573237481968 1.3878308914427424 chr15 102531392 66671869 0.6502581082679537 1.087209484646849 chr16 90354753 74276268 0.8220515859304048 8.042870985016409 chr17 81195210 91925001 1.1321480786859224 7.146792285357553 chr18 78077248 53662613 0.6873015426978164 15.505575951690844 chr19 59128983 54762776 0.9261579215729112 9.626753295593169 chr20 63025520 84614421 1.3425422114724321 2.4235396218569565 chr21 48129895 47063654 0.9778465961747891 3.321268516214117 chr22 51304566 26260957 0.5118639342938794 0.9301778793889874 chrMT 16571 2047237 123.54335887997104 18.581733170278913 chrX 155270560 123350909 0.7944256077906848 3.036303939642229 chrY 59373566 10149420 0.17094172851265158 8.31005652249531