BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617361.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 = 30,050,362 (93.91%) number of supplementary alignments = 66,889 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,104,903 number of mapped paired reads (second in pair) = 14,945,459 number of mapped paired reads (both in pair) = 29,499,524 number of mapped paired reads (singletons) = 550,838 number of mapped bases = 2,951,411,501 bp number of sequenced bases = 2,950,552,431 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,547,853 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 52,369.7709 std insert size = 2,183,127.4032 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.4603 >>>>>>> ACTG content number of A's = 893,878,406 bp (30.3%) number of C's = 586,062,594 bp (19.86%) number of T's = 881,078,767 bp (29.86%) number of G's = 588,568,373 bp (19.95%) number of N's = 964,291 bp (0.03%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 33,929,338 number of insertions = 294,854 mapped reads with insertion percentage = 0.95% number of deletions = 358,472 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.19% >>>>>>> Coverage mean coverageData = 0.9534X std coverageData = 9.7227X There is a 52.82% of reference with a coverageData >= 1X There is a 23.85% of reference with a coverageData >= 2X There is a 9.18% of reference with a coverageData >= 3X There is a 3.23% of reference with a coverageData >= 4X There is a 1.11% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% 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 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% 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 191940426 0.7700700011495658 19.639883036107204 chr2 243199373 291434965 1.1983376494971474 8.744996791330177 chr3 198022430 235199676 1.1877426006740752 1.4594152128326738 chr4 191154276 161442567 0.84456686179492 9.246729088208347 chr5 180915260 185587334 1.025824654039687 1.4608156882292347 chr6 171115067 138539049 0.8096250752717176 3.651683048509724 chr7 159138663 239551170 1.5052983698876494 10.958522289121527 chr8 146364022 124387311 0.8498489540004578 7.5159173941725745 chr9 141213431 124480654 0.8815071846813212 14.791999215353767 chr10 135534747 124273511 0.9169125537969979 20.200679712335234 chr11 135006516 158240361 1.172094249139797 5.570077835240958 chr12 133851895 130060854 0.9716773453226045 1.3582606924778045 chr13 115169878 128563866 1.1162976659574129 1.2908193012427396 chr14 107349540 85526473 0.7967101954978102 1.3625153244190003 chr15 102531392 66589705 0.6494567536935419 0.9761414657320099 chr16 90354753 74059734 0.819655098830274 7.872288943644524 chr17 81195210 91746065 1.1299443033646936 7.11678065911432 chr18 78077248 53287564 0.6824979794369802 15.20053805709588 chr19 59128983 54693226 0.9249816794582785 9.660799440266768 chr20 63025520 84159868 1.335330006003917 2.4303756592098735 chr21 48129895 46922170 0.9749069679042516 3.1957032381748562 chr22 51304566 25998818 0.5067544670390546 0.9063074392936917 chrMT 16571 1969573 118.85661698147366 20.529579318547263 chrX 155270560 122771953 0.7906969164019245 3.018978553226415 chrY 59373566 9984608 0.16816588041890562 8.14815589983294