BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090212.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 = 25,854,184 number of mapped reads = 22,376,715 (86.55%) number of supplementary alignments = 1,023 (0%) number of secondary alignments = 0 number of mapped bases = 1,056,033,063 bp number of sequenced bases = 1,055,834,578 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,187,738 duplication rate = 12.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2613 >>>>>>> ACTG content number of A's = 309,918,762 bp (29.35%) number of C's = 214,749,911 bp (20.34%) number of T's = 304,722,130 bp (28.86%) number of G's = 226,440,623 bp (21.45%) number of N's = 3,152 bp (0%) GC percentage = 41.79% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 4,019,841 number of insertions = 39,465 mapped reads with insertion percentage = 0.18% number of deletions = 130,430 mapped reads with deletion percentage = 0.58% homopolymer indels = 47.13% >>>>>>> Coverage mean coverageData = 0.3411X std coverageData = 2.1046X There is a 14.72% of reference with a coverageData >= 1X There is a 7.4% of reference with a coverageData >= 2X There is a 4.16% of reference with a coverageData >= 3X There is a 2.49% of reference with a coverageData >= 4X There is a 1.55% of reference with a coverageData >= 5X There is a 0.99% of reference with a coverageData >= 6X There is a 0.65% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% 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 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 88528943 0.355180431024884 3.151068256020652 chr2 243199373 100892466 0.41485495935057365 2.3623842415834986 chr3 198022430 96196045 0.4857835801732157 1.4395109857036732 chr4 191154276 56539061 0.29577711879173446 1.1118370802165345 chr5 180915260 47399847 0.26200027018174143 1.017208272505989 chr6 171115067 58724571 0.3431876107087636 1.4021539631169124 chr7 159138663 77294201 0.48570347106661316 3.878271678565236 chr8 146364022 95601907 0.6531790100712045 4.219747442253654 chr9 141213431 33280948 0.23567834705467924 1.7705773516296623 chr10 135534747 32884466 0.2426275676745831 1.728143232722236 chr11 135006516 45704454 0.33853517114685044 1.8033099427577728 chr12 133851895 38014566 0.2840046904080066 1.1134055770323175 chr13 115169878 32214550 0.2797133292092226 1.0329807826947386 chr14 107349540 35759504 0.33311278278416473 1.197558566372243 chr15 102531392 27588441 0.26907311470032513 1.0201685601648074 chr16 90354753 22116566 0.24477479341900255 1.1364310980856076 chr17 81195210 23030521 0.28364383810325755 1.238236539847814 chr18 78077248 35815396 0.4587174486477802 2.8152458763688877 chr19 59128983 19518546 0.3301011620646342 2.2832252999084064 chr20 63025520 26364476 0.41831429554250404 1.3822060532690217 chr21 48129895 16022830 0.3329080605723324 1.3533020885091918 chr22 51304566 8983598 0.17510328417942372 0.8007616707041617 chrMT 16571 579068 34.94466236195764 22.07891048491519 chrX 155270560 34209623 0.22032266129522557 1.233939565964976 chrY 59373566 2768469 0.046627972454947375 1.6363771958932987