BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004127.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,826,202 number of mapped reads = 3,916,368 (81.15%) number of supplementary alignments = 26,471 (0.55%) number of secondary alignments = 0 number of mapped bases = 265,039,967 bp number of sequenced bases = 264,916,154 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 202,971 duplication rate = 3.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3781 >>>>>>> ACTG content number of A's = 74,623,597 bp (28.17%) number of C's = 48,215,212 bp (18.2%) number of T's = 84,811,664 bp (32.01%) number of G's = 57,237,164 bp (21.61%) number of N's = 28,517 bp (0.01%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 2,526,626 number of insertions = 23,464 mapped reads with insertion percentage = 0.59% number of deletions = 73,477 mapped reads with deletion percentage = 1.85% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.0856X std coverageData = 0.7572X There is a 6.73% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 17574997 0.07051134689048578 1.409560936058168 chr2 243199373 21938689 0.0902086577336694 0.8653851734028818 chr3 198022430 16207557 0.08184707661652268 0.34799645260074424 chr4 191154276 13474616 0.07049079038127298 0.3460041801266551 chr5 180915260 12393354 0.0685036408758443 0.32582936609235796 chr6 171115067 18133438 0.10597218770922143 0.5060590898209878 chr7 159138663 20352974 0.12789458963847145 1.2798248656659952 chr8 146364022 19921820 0.13611145504050168 1.1956352788320128 chr9 141213431 7394675 0.05236523854448377 0.6014955583654511 chr10 135534747 11529817 0.08506908564192768 0.6529428627858432 chr11 135006516 13451889 0.09963881298884862 0.6056828504710348 chr12 133851895 14034882 0.10485381622725626 0.40217720122874306 chr13 115169878 10664567 0.09259857859708769 0.3635688736971144 chr14 107349540 7715840 0.07187585526682276 0.3932690754931006 chr15 102531392 7050215 0.06876152622603622 0.32516848397966736 chr16 90354753 7197598 0.07965931797743944 0.44616712165485056 chr17 81195210 6683185 0.08231008947448994 0.4219284638544247 chr18 78077248 7565906 0.09690282628813966 1.3956463411463744 chr19 59128983 4724376 0.07989949700301796 0.9450615807478524 chr20 63025520 6622049 0.10506932747242705 0.4453892860610356 chr21 48129895 4192164 0.08710104187844166 0.3974309857609804 chr22 51304566 2127762 0.041473150752313157 0.24161121297411645 chrMT 16571 109891 6.6315249532315494 4.775655015334539 chrX 155270560 13346997 0.08595961140347533 0.4344972547105485 chrY 59373566 630709 0.010622723923976538 0.20447147780747094