BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617413.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 = 28,615,241 (89.42%) number of supplementary alignments = 402,186 (1.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,636,623 number of mapped paired reads (second in pair) = 13,978,618 number of mapped paired reads (both in pair) = 27,699,582 number of mapped paired reads (singletons) = 915,659 number of mapped bases = 2,798,472,767 bp number of sequenced bases = 2,797,870,606 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,239,171 duplication rate = 3.97% >>>>>>> Insert size mean insert size = 47,530.4686 std insert size = 2,071,440.5798 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.7193 >>>>>>> ACTG content number of A's = 836,113,737 bp (29.88%) number of C's = 561,208,393 bp (20.06%) number of T's = 826,619,035 bp (29.54%) number of G's = 572,790,695 bp (20.47%) number of N's = 1,138,746 bp (0.04%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0153 number of mismatches = 42,419,853 number of insertions = 231,013 mapped reads with insertion percentage = 0.79% number of deletions = 270,930 mapped reads with deletion percentage = 0.93% homopolymer indels = 43.95% >>>>>>> Coverage mean coverageData = 0.904X std coverageData = 2.7624X There is a 28.92% of reference with a coverageData >= 1X There is a 16.36% of reference with a coverageData >= 2X There is a 10.35% of reference with a coverageData >= 3X There is a 7.1% of reference with a coverageData >= 4X There is a 5.12% of reference with a coverageData >= 5X There is a 3.83% of reference with a coverageData >= 6X There is a 2.95% of reference with a coverageData >= 7X There is a 2.32% of reference with a coverageData >= 8X There is a 1.86% of reference with a coverageData >= 9X There is a 1.51% of reference with a coverageData >= 10X There is a 1.25% of reference with a coverageData >= 11X There is a 1.04% of reference with a coverageData >= 12X There is a 0.88% of reference with a coverageData >= 13X There is a 0.75% of reference with a coverageData >= 14X There is a 0.64% of reference with a coverageData >= 15X There is a 0.55% of reference with a coverageData >= 16X There is a 0.48% of reference with a coverageData >= 17X There is a 0.42% of reference with a coverageData >= 18X There is a 0.37% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.16% of reference with a coverageData >= 26X There is a 0.15% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 180079149 0.7224822480983909 2.5859642305017725 chr2 243199373 279608515 1.1497090290606957 2.9108177931735293 chr3 198022430 236701457 1.195326494074434 3.2312460889029793 chr4 191154276 135263093 0.7076121749952379 2.172081343881331 chr5 180915260 179442525 0.9918595313629154 2.7243989594174454 chr6 171115067 128566955 0.7513479511421399 2.4699441835307048 chr7 159138663 209339498 1.3154534168733087 3.0666793710215456 chr8 146364022 123806830 0.8458829451953704 3.061346170784667 chr9 141213431 112096307 0.7938076867490034 2.462462662077626 chr10 135534747 89647671 0.6614368122146567 2.2844614838117305 chr11 135006516 207637112 1.5379784483883725 3.6257636371114432 chr12 133851895 133399371 0.9966192185773687 2.629885068578203 chr13 115169878 122061654 1.0598400911738397 2.6417627177157508 chr14 107349540 80896284 0.7535783013136339 2.72841713090544 chr15 102531392 63906040 0.62328267229611 2.210937412165224 chr16 90354753 69982393 0.7745291827647407 3.1168620026502 chr17 81195210 85348783 1.0511553945115728 3.4415044238547967 chr18 78077248 40241539 0.5154067289871692 1.8822718832799674 chr19 59128983 39474903 0.6676066625397565 2.186238275512472 chr20 63025520 94722640 1.5029251642826589 4.445100624026325 chr21 48129895 38241878 0.7945556083178656 2.383217603094909 chr22 51304566 22392793 0.43646783796982125 1.9504996746707672 chrMT 16571 171897 10.373363104218212 5.612128361303874 chrX 155270560 123240232 0.793712806857913 2.4282106121332565 chrY 59373566 2203248 0.037108230959211716 0.5132639578492648