BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777252.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 59,851,126 number of mapped reads = 59,652,972 (99.67%) number of supplementary alignments = 1,988,421 (3.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,825,624 number of mapped paired reads (second in pair) = 29,827,348 number of mapped paired reads (both in pair) = 59,613,294 number of mapped paired reads (singletons) = 39,678 number of mapped bases = 5,985,118,029 bp number of sequenced bases = 5,984,210,936 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,775,407 duplication rate = 47.69% >>>>>>> Insert size mean insert size = 200,710.6263 std insert size = 4,326,739.7991 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 54.7766 >>>>>>> ACTG content number of A's = 1,681,509,828 bp (28.1%) number of C's = 1,309,864,504 bp (21.89%) number of T's = 1,666,867,405 bp (27.85%) number of G's = 1,325,895,136 bp (22.16%) number of N's = 74,063 bp (0%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 12,860,906 number of insertions = 982,521 mapped reads with insertion percentage = 1.62% number of deletions = 404,178 mapped reads with deletion percentage = 0.66% homopolymer indels = 50.66% >>>>>>> Coverage mean coverageData = 1.9334X std coverageData = 19.513X There is a 16.94% of reference with a coverageData >= 1X There is a 9.89% of reference with a coverageData >= 2X There is a 6.35% of reference with a coverageData >= 3X There is a 4.79% of reference with a coverageData >= 4X There is a 3.86% of reference with a coverageData >= 5X There is a 3.35% of reference with a coverageData >= 6X There is a 2.99% of reference with a coverageData >= 7X There is a 2.74% of reference with a coverageData >= 8X There is a 2.54% of reference with a coverageData >= 9X There is a 2.39% of reference with a coverageData >= 10X There is a 2.26% of reference with a coverageData >= 11X There is a 2.16% of reference with a coverageData >= 12X There is a 2.06% of reference with a coverageData >= 13X There is a 1.98% of reference with a coverageData >= 14X There is a 1.9% of reference with a coverageData >= 15X There is a 1.84% of reference with a coverageData >= 16X There is a 1.77% of reference with a coverageData >= 17X There is a 1.72% of reference with a coverageData >= 18X There is a 1.66% of reference with a coverageData >= 19X There is a 1.61% of reference with a coverageData >= 20X There is a 1.57% of reference with a coverageData >= 21X There is a 1.52% of reference with a coverageData >= 22X There is a 1.48% of reference with a coverageData >= 23X There is a 1.44% of reference with a coverageData >= 24X There is a 1.41% of reference with a coverageData >= 25X There is a 1.37% of reference with a coverageData >= 26X There is a 1.34% of reference with a coverageData >= 27X There is a 1.31% of reference with a coverageData >= 28X There is a 1.28% of reference with a coverageData >= 29X There is a 1.25% of reference with a coverageData >= 30X There is a 1.22% of reference with a coverageData >= 31X There is a 1.19% of reference with a coverageData >= 32X There is a 1.17% of reference with a coverageData >= 33X There is a 1.14% of reference with a coverageData >= 34X There is a 1.12% of reference with a coverageData >= 35X There is a 1.1% of reference with a coverageData >= 36X There is a 1.08% of reference with a coverageData >= 37X There is a 1.06% of reference with a coverageData >= 38X There is a 1.04% of reference with a coverageData >= 39X There is a 1.02% of reference with a coverageData >= 40X There is a 1% of reference with a coverageData >= 41X There is a 0.98% of reference with a coverageData >= 42X There is a 0.96% of reference with a coverageData >= 43X There is a 0.94% of reference with a coverageData >= 44X There is a 0.93% of reference with a coverageData >= 45X There is a 0.91% of reference with a coverageData >= 46X There is a 0.9% of reference with a coverageData >= 47X There is a 0.88% of reference with a coverageData >= 48X There is a 0.87% of reference with a coverageData >= 49X There is a 0.85% of reference with a coverageData >= 50X There is a 0.84% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 588110700 2.3595154854197937 20.768599729653317 chr2 243199373 548065859 2.2535660854684854 20.6365044890243 chr3 198022430 374833857 1.8928858564153566 18.44192280474191 chr4 191154276 282934035 1.4801344804863272 16.66279617298229 chr5 180915260 315202150 1.7422640301321182 17.653288446475532 chr6 171115067 281325002 1.6440691455884477 16.68668446560438 chr7 159138663 400873558 2.519020522372995 24.632976154220565 chr8 146364022 208625657 1.4253889319876711 17.16290832905013 chr9 141213431 228410873 1.6174868876318145 22.85649370041476 chr10 135534747 257378170 1.8989829228072415 17.950155613058442 chr11 135006516 419620166 3.108147506006303 27.646084181643293 chr12 133851895 340205079 2.5416530636342505 21.807178079665803 chr13 115169878 191214594 1.6602830299082196 19.15975995633238 chr14 107349540 133194423 1.2407544829721673 13.414970521642154 chr15 102531392 285814743 2.7875827824516417 25.364441501098323 chr16 90354753 171904752 1.902553504849933 17.26300475989427 chr17 81195210 241417197 2.9732935846831356 23.15088325110559 chr18 78077248 94936549 1.2159310353766568 13.60190347051799 chr19 59128983 191557239 3.239650494242392 23.07478803930665 chr20 63025520 158885339 2.5209683156918024 23.017713026100303 chr21 48129895 39235502 0.815200240931338 12.309897139688198 chr22 51304566 55712771 1.0859222744423955 10.872146837115134 chrMT 16571 1322065 79.78184780640879 42.65076519567886 chrX 155270560 172788888 1.1128245302908677 13.204221982412442 chrY 59373566 1548861 0.026086710035236892 0.9526267615279483