BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618668.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 = 23,167,464 number of mapped reads = 21,049,955 (90.86%) number of supplementary alignments = 89,524 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,457,961 number of mapped paired reads (second in pair) = 10,591,994 number of mapped paired reads (both in pair) = 20,491,290 number of mapped paired reads (singletons) = 558,665 number of mapped bases = 2,035,147,174 bp number of sequenced bases = 2,034,516,031 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,270,540 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 58,865.5361 std insert size = 2,416,875.2425 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 53.4315 >>>>>>> ACTG content number of A's = 601,180,079 bp (29.55%) number of C's = 416,779,241 bp (20.49%) number of T's = 596,683,680 bp (29.33%) number of G's = 418,134,002 bp (20.55%) number of N's = 1,739,029 bp (0.09%) GC percentage = 41.04% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 16,916,735 number of insertions = 216,027 mapped reads with insertion percentage = 0.99% number of deletions = 255,479 mapped reads with deletion percentage = 1.17% homopolymer indels = 40.87% >>>>>>> Coverage mean coverageData = 0.6574X std coverageData = 6.5406X There is a 39.85% of reference with a coverageData >= 1X There is a 15.71% of reference with a coverageData >= 2X There is a 4.98% of reference with a coverageData >= 3X There is a 1.59% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 166641785 0.6685711928477001 14.475681505134913 chr2 243199373 176911342 0.7274333803483942 5.927502783317678 chr3 198022430 135952371 0.6865503619968708 1.2175177777517134 chr4 191154276 137864222 0.7212196602915647 3.8079966550915074 chr5 180915260 124223028 0.6866365391178169 1.1265512999661491 chr6 171115067 118444234 0.692190559700976 2.9124254311136015 chr7 159138663 110779681 0.6961204707368944 4.536616491460404 chr8 146364022 104239261 0.7121918322249986 8.141700242932027 chr9 141213431 87493825 0.6195857177353052 6.478178693886936 chr10 135534747 105820575 0.780763437733056 14.935912863661782 chr11 135006516 94026734 0.6964607100889856 3.431788442183548 chr12 133851895 90501661 0.6761328332333285 1.1025430027056837 chr13 115169878 66381401 0.5763781481126514 0.9635155752343685 chr14 107349540 62473927 0.5819673470421951 1.244931867452357 chr15 102531392 58153259 0.5671751632904779 1.0075984137205451 chr16 90354753 63873897 0.7069234863604795 4.929026326774646 chr17 81195210 56165438 0.6917333916618973 2.9431788995011225 chr18 78077248 57116313 0.7315359398937832 8.207034902201622 chr19 59128983 40759620 0.6893340276121441 6.383401357257306 chr20 63025520 42844124 0.6797900913788574 2.3639986712145635 chr21 48129895 29110683 0.6048357886506921 3.505879802021366 chr22 51304566 25800785 0.5028945181994133 3.160620431088796 chrMT 16571 920831 55.56882505582041 12.277584344989602 chrX 155270560 55112370 0.35494410530882353 1.619020712280929 chrY 59373566 23535807 0.3964021126842878 7.263661763979674