BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975254.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 148,961,592 number of mapped reads = 148,340,632 (99.58%) number of supplementary alignments = 269,807 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 74,149,815 number of mapped paired reads (second in pair) = 74,190,817 number of mapped paired reads (both in pair) = 148,093,766 number of mapped paired reads (singletons) = 246,866 number of mapped bases = 13,498,681,388 bp number of sequenced bases = 13,493,861,236 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,877,488 duplication rate = 46.35% >>>>>>> Insert size mean insert size = 78,379.2483 std insert size = 2,760,639.2406 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 55.6908 >>>>>>> ACTG content number of A's = 3,529,702,464 bp (26.16%) number of C's = 3,035,180,285 bp (22.49%) number of T's = 3,646,196,357 bp (27.02%) number of G's = 3,282,415,182 bp (24.33%) number of N's = 366,948 bp (0%) GC percentage = 46.82% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 92,468,558 number of insertions = 1,464,848 mapped reads with insertion percentage = 0.98% number of deletions = 3,421,303 mapped reads with deletion percentage = 2.27% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 4.3605X std coverageData = 58.8315X There is a 28.46% of reference with a coverageData >= 1X There is a 18.24% of reference with a coverageData >= 2X There is a 12.16% of reference with a coverageData >= 3X There is a 8.98% of reference with a coverageData >= 4X There is a 6.8% of reference with a coverageData >= 5X There is a 5.47% of reference with a coverageData >= 6X There is a 4.5% of reference with a coverageData >= 7X There is a 3.85% of reference with a coverageData >= 8X There is a 3.36% of reference with a coverageData >= 9X There is a 3.01% of reference with a coverageData >= 10X There is a 2.73% of reference with a coverageData >= 11X There is a 2.52% of reference with a coverageData >= 12X There is a 2.35% of reference with a coverageData >= 13X There is a 2.21% of reference with a coverageData >= 14X There is a 2.1% of reference with a coverageData >= 15X There is a 2.01% of reference with a coverageData >= 16X There is a 1.93% of reference with a coverageData >= 17X There is a 1.86% of reference with a coverageData >= 18X There is a 1.8% of reference with a coverageData >= 19X There is a 1.75% of reference with a coverageData >= 20X There is a 1.7% of reference with a coverageData >= 21X There is a 1.66% of reference with a coverageData >= 22X There is a 1.62% of reference with a coverageData >= 23X There is a 1.59% of reference with a coverageData >= 24X There is a 1.55% of reference with a coverageData >= 25X There is a 1.52% of reference with a coverageData >= 26X There is a 1.5% of reference with a coverageData >= 27X There is a 1.47% of reference with a coverageData >= 28X There is a 1.45% of reference with a coverageData >= 29X There is a 1.42% of reference with a coverageData >= 30X There is a 1.4% of reference with a coverageData >= 31X There is a 1.38% of reference with a coverageData >= 32X There is a 1.36% of reference with a coverageData >= 33X There is a 1.34% of reference with a coverageData >= 34X There is a 1.32% of reference with a coverageData >= 35X There is a 1.31% of reference with a coverageData >= 36X There is a 1.29% of reference with a coverageData >= 37X There is a 1.27% of reference with a coverageData >= 38X There is a 1.26% of reference with a coverageData >= 39X There is a 1.24% of reference with a coverageData >= 40X There is a 1.23% of reference with a coverageData >= 41X There is a 1.21% of reference with a coverageData >= 42X There is a 1.2% of reference with a coverageData >= 43X There is a 1.19% of reference with a coverageData >= 44X There is a 1.17% of reference with a coverageData >= 45X There is a 1.16% of reference with a coverageData >= 46X There is a 1.15% of reference with a coverageData >= 47X There is a 1.14% of reference with a coverageData >= 48X There is a 1.12% of reference with a coverageData >= 49X There is a 1.11% of reference with a coverageData >= 50X There is a 1.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1387622909 5.567179345161993 69.77078098492001 chr2 243199373 1030961223 4.239160694711166 53.209077082835464 chr3 198022430 737613480 3.7248986390077126 50.92799717761986 chr4 191154276 496127711 2.5954308811799742 40.53687769259425 chr5 180915260 677357746 3.744060871371492 50.960814742866084 chr6 171115067 1211632314 7.0808043689104245 88.45556961949914 chr7 159138663 651732522 4.0953751257794595 59.69145200308677 chr8 146364022 580582987 3.966705608841495 50.61466367002729 chr9 141213431 482764700 3.4186882691066405 46.51718771226654 chr10 135534747 545199323 4.022579707918 53.84207726256654 chr11 135006516 845460389 6.26236728455388 73.53056510546969 chr12 133851895 796161080 5.948074773240976 72.25685203891832 chr13 115169878 276660250 2.4021927851655795 36.87006774174032 chr14 107349540 399693223 3.723287710408447 53.16195312802925 chr15 102531392 374087792 3.64851958705486 50.309631785795354 chr16 90354753 504875448 5.587702154417931 71.0603932888478 chr17 81195210 631253546 7.7745170681866576 78.18080786679735 chr18 78077248 307491133 3.9382936883226214 57.03824033270985 chr19 59128983 445370607 7.532187844326699 78.18536619474042 chr20 63025520 375955926 5.965138026627944 72.08149285946439 chr21 48129895 145477050 3.022592299442997 46.74166642870915 chr22 51304566 206244486 4.0200025471417105 55.68834566084817 chrMT 16571 502246 30.308732122382477 34.25025023204673 chrX 155270560 372376627 2.3982436013626796 37.511646599230254 chrY 59373566 15476670 0.2606660007586541 5.6636162568449695