BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618588.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 57,255,644 number of mapped reads = 55,006,413 (96.07%) number of supplementary alignments = 234,622 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,804,139 number of mapped paired reads (second in pair) = 27,202,274 number of mapped paired reads (both in pair) = 54,117,380 number of mapped paired reads (singletons) = 889,033 number of mapped bases = 5,257,628,636 bp number of sequenced bases = 5,253,698,900 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,527,078 duplication rate = 29.27% >>>>>>> Insert size mean insert size = 81,221.9085 std insert size = 2,820,596.9577 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.8392 >>>>>>> ACTG content number of A's = 1,411,132,830 bp (26.86%) number of C's = 1,182,505,201 bp (22.51%) number of T's = 1,412,566,113 bp (26.89%) number of G's = 1,247,240,402 bp (23.74%) number of N's = 254,354 bp (0%) GC percentage = 46.25% >>>>>>> Mismatches and indels general error rate = 0.0134 number of mismatches = 68,586,982 number of insertions = 1,007,754 mapped reads with insertion percentage = 1.79% number of deletions = 2,733,182 mapped reads with deletion percentage = 4.84% homopolymer indels = 51.17% >>>>>>> Coverage mean coverageData = 1.6984X std coverageData = 7.8352X There is a 24.89% of reference with a coverageData >= 1X There is a 18.44% of reference with a coverageData >= 2X There is a 14.6% of reference with a coverageData >= 3X There is a 11.98% of reference with a coverageData >= 4X There is a 10.02% of reference with a coverageData >= 5X There is a 8.52% of reference with a coverageData >= 6X There is a 7.32% of reference with a coverageData >= 7X There is a 6.36% of reference with a coverageData >= 8X There is a 5.56% of reference with a coverageData >= 9X There is a 4.9% of reference with a coverageData >= 10X There is a 4.35% of reference with a coverageData >= 11X There is a 3.88% of reference with a coverageData >= 12X There is a 3.47% of reference with a coverageData >= 13X There is a 3.13% of reference with a coverageData >= 14X There is a 2.82% of reference with a coverageData >= 15X There is a 2.56% of reference with a coverageData >= 16X There is a 2.33% of reference with a coverageData >= 17X There is a 2.12% of reference with a coverageData >= 18X There is a 1.94% of reference with a coverageData >= 19X There is a 1.78% of reference with a coverageData >= 20X There is a 1.64% of reference with a coverageData >= 21X There is a 1.51% of reference with a coverageData >= 22X There is a 1.39% of reference with a coverageData >= 23X There is a 1.28% of reference with a coverageData >= 24X There is a 1.19% of reference with a coverageData >= 25X There is a 1.1% of reference with a coverageData >= 26X There is a 1.02% of reference with a coverageData >= 27X There is a 0.95% of reference with a coverageData >= 28X There is a 0.89% of reference with a coverageData >= 29X There is a 0.83% of reference with a coverageData >= 30X There is a 0.77% of reference with a coverageData >= 31X There is a 0.72% of reference with a coverageData >= 32X There is a 0.67% of reference with a coverageData >= 33X There is a 0.63% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.56% of reference with a coverageData >= 36X There is a 0.52% of reference with a coverageData >= 37X There is a 0.49% of reference with a coverageData >= 38X There is a 0.46% of reference with a coverageData >= 39X There is a 0.44% of reference with a coverageData >= 40X There is a 0.41% of reference with a coverageData >= 41X There is a 0.39% of reference with a coverageData >= 42X There is a 0.37% of reference with a coverageData >= 43X There is a 0.35% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.31% of reference with a coverageData >= 46X There is a 0.29% of reference with a coverageData >= 47X There is a 0.28% of reference with a coverageData >= 48X There is a 0.27% of reference with a coverageData >= 49X There is a 0.25% of reference with a coverageData >= 50X There is a 0.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 472657567 1.8963145010579532 7.601723427409813 chr2 243199373 445380468 1.8313388826047672 10.759238119445516 chr3 198022430 327112717 1.6518972976950137 5.608740339809028 chr4 191154276 261843675 1.3698028654090897 9.407371263148718 chr5 180915260 287022985 1.586505112946249 5.595549165322129 chr6 171115067 271679549 1.5877009182364987 5.93576975163232 chr7 159138663 255407232 1.6049351376038643 5.9474882729405 chr8 146364022 258551492 1.7664962226851078 6.438738534306477 chr9 141213431 232756073 1.6482573318397737 9.701956588262377 chr10 135534747 270612921 1.9966313214130986 10.692051676341407 chr11 135006516 261170629 1.9345038797979204 6.808644629751888 chr12 133851895 232999287 1.7407246046086984 6.584432269113494 chr13 115169878 131614357 1.1427845482305712 4.504848306639552 chr14 107349540 157105745 1.4634971421395937 5.650225629989756 chr15 102531392 172893972 1.6862540206222891 6.1341093524048445 chr16 90354753 190186320 2.1048845100600295 10.749839921868013 chr17 81195210 174164954 2.1450151308186776 8.331146750247477 chr18 78077248 132561713 1.6978276821437148 11.099663925314932 chr19 59128983 114795384 1.941440190168669 7.269646325472917 chr20 63025520 156820895 2.488212631962418 8.177366867672058 chr21 48129895 66478287 1.3812265121293117 11.17056733565297 chr22 51304566 102579818 1.9994286278535132 7.613817897403523 chrMT 16571 34367 2.073924325629111 8.166107063029724 chrX 155270560 270043482 1.7391801897281751 5.712550483846117 chrY 59373566 11154747 0.1878739606106866 7.1962385667568105