BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10251055.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP224945/SRP224945.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 = 4,213,342 number of mapped reads = 4,006,851 (95.1%) number of supplementary alignments = 35,103 (0.83%) number of secondary alignments = 0 number of mapped bases = 311,006,716 bp number of sequenced bases = 310,810,022 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,016,685 duplication rate = 22.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0994 >>>>>>> ACTG content number of A's = 90,897,302 bp (29.25%) number of C's = 61,924,723 bp (19.92%) number of T's = 92,083,902 bp (29.63%) number of G's = 65,901,517 bp (21.2%) number of N's = 2,578 bp (0%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,855,580 number of insertions = 37,526 mapped reads with insertion percentage = 0.92% number of deletions = 109,701 mapped reads with deletion percentage = 2.69% homopolymer indels = 44.95% >>>>>>> Coverage mean coverageData = 0.1005X std coverageData = 1.093X There is a 6.18% of reference with a coverageData >= 1X There is a 2.16% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 24883706 0.0998340782468903 2.339966613605312 chr2 243199373 26351542 0.10835365928348836 1.2202214388783803 chr3 198022430 20409122 0.10306469827685683 0.47840810903143904 chr4 191154276 19488950 0.10195403633031991 0.5431183306489127 chr5 180915260 18898044 0.10445798767887242 0.49350254460975446 chr6 171115067 17793704 0.10398677516808032 0.6721293450234392 chr7 159138663 16979237 0.10669460632580531 1.6574316274022278 chr8 146364022 15375474 0.10504954557753271 0.7356192454237894 chr9 141213431 13087579 0.09267942084064228 1.240929911806474 chr10 135534747 18169680 0.13405920180748926 1.1519188623571615 chr11 135006516 14121925 0.10460180307149027 0.6665296116931346 chr12 133851895 13650222 0.1019800429422385 0.4950696376824673 chr13 115169878 9781428 0.08493043641150684 0.4261981895803894 chr14 107349540 9285415 0.08649701712741387 0.709126350813004 chr15 102531392 8723925 0.08508540486800374 0.4298557956944812 chr16 90354753 8791537 0.0973002161823186 0.7880811056102377 chr17 81195210 8030343 0.0989016839786485 0.6106488201314506 chr18 78077248 8276498 0.10600396673817192 1.3563241838539466 chr19 59128983 6233199 0.10541698307241307 2.1714325633697906 chr20 63025520 6246934 0.09911753207272228 0.5151080476479752 chr21 48129895 4083889 0.0848514005692304 0.486496527806619 chr22 51304566 3388594 0.06604858522728757 0.39629363048839167 chrMT 16571 310926 18.76326111882204 10.51798494634941 chrX 155270560 17684855 0.11389702593975316 0.5962165821109333 chrY 59373566 959988 0.016168609444815896 0.8164496194431243