BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504751.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 1,761,989 number of mapped reads = 1,607,851 (91.25%) number of secondary alignments = 0 number of mapped bases = 51,446,292 bp number of sequenced bases = 51,446,292 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 307,994 duplication rate = 9.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.5836 >>>>>>> ACTG content number of A's = 14,791,760 bp (28.75%) number of C's = 10,523,250 bp (20.45%) number of T's = 15,483,163 bp (30.1%) number of G's = 10,647,855 bp (20.7%) number of N's = 264 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 25,909 >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 0.8106X There is a 0.86% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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% 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 3569488 0.01432087906412879 0.28930674109091314 chr2 243199373 3515836 0.014456599770921284 0.24297741920927837 chr3 198022430 2997642 0.015137891197476973 0.24486334224523612 chr4 191154276 5579592 0.029188946837893387 1.0617312257531137 chr5 180915260 2345024 0.012962002210316587 0.1881461390159302 chr6 171115067 5081146 0.029694322592878394 2.1141706734152503 chr7 159138663 2065174 0.012977198382017323 0.20106984001638825 chr8 146364022 3150228 0.021523240185351015 0.5632558986974981 chr9 141213431 1558142 0.011033950446257481 0.17084512297793925 chr10 135534747 1953612 0.014414104451015798 0.32538031889763286 chr11 135006516 1777844 0.013168579211391545 0.1874950913792947 chr12 133851895 2899440 0.021661553614911466 0.498112218466759 chr13 115169878 1351112 0.011731470272114033 0.17087811943444228 chr14 107349540 2420354 0.02254647760949884 0.6121835660567831 chr15 102531392 948382 0.009249674480182615 0.16850367143323725 chr16 90354753 997450 0.011039264309648437 0.18525340542574448 chr17 81195210 803508 0.009896002485860927 0.15676950405913667 chr18 78077248 4710520 0.06033153217695378 3.234913209288726 chr19 59128983 575346 0.009730355078151776 0.18443125295601695 chr20 63025520 995036 0.01578782689932586 0.4419421451702579 chr21 48129895 567030 0.011781243237700809 0.2206871573752287 chr22 51304566 255016 0.004970629709644167 0.09515874332423267 chrMT 16571 96 0.005793253273791563 0.0949652381495725 chrX 155270560 642384 0.004137191235737155 0.11364795161008176 chrY 59373566 686890 0.011568953092694482 0.23064364623070435