BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617497.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 = 30,773,423 (96.17%) number of supplementary alignments = 139,975 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,438,476 number of mapped paired reads (second in pair) = 15,334,947 number of mapped paired reads (both in pair) = 30,398,404 number of mapped paired reads (singletons) = 375,019 number of mapped bases = 3,011,147,188 bp number of sequenced bases = 3,009,352,913 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,406,481 duplication rate = 10.05% >>>>>>> Insert size mean insert size = 29,888.3177 std insert size = 1,604,412.9068 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 52.8319 >>>>>>> ACTG content number of A's = 886,912,707 bp (29.47%) number of C's = 608,927,461 bp (20.23%) number of T's = 887,097,173 bp (29.48%) number of G's = 624,562,641 bp (20.75%) number of N's = 1,852,931 bp (0.06%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 34,771,984 number of insertions = 446,933 mapped reads with insertion percentage = 1.42% number of deletions = 1,051,671 mapped reads with deletion percentage = 3.35% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.9727X std coverageData = 9.7999X There is a 38.48% of reference with a coverageData >= 1X There is a 20.86% of reference with a coverageData >= 2X There is a 11.83% of reference with a coverageData >= 3X There is a 7.06% of reference with a coverageData >= 4X There is a 4.37% of reference with a coverageData >= 5X There is a 2.81% of reference with a coverageData >= 6X There is a 1.86% of reference with a coverageData >= 7X There is a 1.28% of reference with a coverageData >= 8X There is a 0.9% of reference with a coverageData >= 9X There is a 0.65% of reference with a coverageData >= 10X There is a 0.48% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% 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 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% 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 193316648 0.775591439750114 9.372425219511825 chr2 243199373 311455730 1.2806600862412585 11.669482437416427 chr3 198022430 248724187 1.2560404748088385 2.252251325751633 chr4 191154276 155652059 0.8142745339371849 6.295769654957211 chr5 180915260 192868586 1.06607140823831 2.098476997271292 chr6 171115067 141527436 0.8270892708705774 5.509062495756206 chr7 159138663 232579337 1.4614885698769506 13.22401442512246 chr8 146364022 133924918 0.9150125568426919 3.8944060365446567 chr9 141213431 124788922 0.8836901781672595 18.641350456429272 chr10 135534747 127531819 0.9409529424952555 18.796331288566325 chr11 135006516 169846387 1.2580606627905278 12.746982414534143 chr12 133851895 131417578 0.9818133542300616 2.0027243708075244 chr13 115169878 127692075 1.108728056480185 2.140093710652306 chr14 107349540 87582879 0.8158663651469769 2.217857458940031 chr15 102531392 67995799 0.6631705439052266 1.4636213644055998 chr16 90354753 81209517 0.898785224945499 14.921571709065173 chr17 81195210 84271362 1.0378858802138697 13.85000219062793 chr18 78077248 53945359 0.6909229049671423 17.17559560861969 chr19 59128983 35954000 0.6080605174623078 5.884742912136355 chr20 63025520 89228283 1.4157484618928968 2.807019708670737 chr21 48129895 43365560 0.9010108997744541 3.8805692767110487 chr22 51304566 22574238 0.44000446276068295 1.259071498376075 chrMT 16571 2151509 129.83579747752097 93.05079489687868 chrX 155270560 141162010 0.9091357047981279 4.181489945811828 chrY 59373566 10380990 0.17484194902492467 13.94819422589152