BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231816.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 = 5,385,335 number of mapped reads = 5,138,845 (95.42%) number of supplementary alignments = 29,591 (0.55%) number of secondary alignments = 0 number of mapped bases = 343,187,481 bp number of sequenced bases = 343,062,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 474,422 duplication rate = 7.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9966 >>>>>>> ACTG content number of A's = 93,770,970 bp (27.33%) number of C's = 63,457,971 bp (18.5%) number of T's = 109,249,730 bp (31.85%) number of G's = 76,444,158 bp (22.28%) number of N's = 139,421 bp (0.04%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 2,025,576 number of insertions = 23,349 mapped reads with insertion percentage = 0.45% number of deletions = 69,992 mapped reads with deletion percentage = 1.35% homopolymer indels = 45.57% >>>>>>> Coverage mean coverageData = 0.1109X std coverageData = 0.9667X There is a 7.95% of reference with a coverageData >= 1X There is a 2.05% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 42590217 0.17087306273953073 2.034816180585367 chr2 243199373 13358797 0.05492940559513696 0.9388629396478119 chr3 198022430 39298142 0.1984529833312317 0.5948405005658133 chr4 191154276 10340251 0.054093746770278894 0.3679425366436914 chr5 180915260 21848832 0.12076831993055755 0.4578604973947549 chr6 171115067 25603261 0.14962598822463716 0.6929518667485981 chr7 159138663 25203986 0.15837751508569606 1.44392058547977 chr8 146364022 17142435 0.11712191811728158 1.7254481776164323 chr9 141213431 8589364 0.06082540406514165 0.5681006614905485 chr10 135534747 15619748 0.11524534000126181 0.7060537531464401 chr11 135006516 7779644 0.057624211263995584 0.4988186205063125 chr12 133851895 11818412 0.08829469317561772 0.39824107258992564 chr13 115169878 21042640 0.18270957966978135 0.5844517556165804 chr14 107349540 11898772 0.11084138786249108 0.5146853381883435 chr15 102531392 8906222 0.08686336766012111 0.420607795466891 chr16 90354753 8319520 0.09207617445426473 0.4915518845903731 chr17 81195210 6917878 0.08520056786601081 0.4291911301890135 chr18 78077248 6082715 0.07790637036797199 1.5748208154330352 chr19 59128983 6220630 0.10520441388278233 1.2309813503677476 chr20 63025520 9955399 0.15795822073344257 0.5901713336102579 chr21 48129895 4274356 0.0888087538940195 0.41951674869005035 chr22 51304566 2771908 0.05402848549581338 0.2902361346609783 chrMT 16571 234732 14.165228411079596 9.064874994139997 chrX 155270560 16656085 0.1072713655441186 0.5081857980859782 chrY 59373566 713535 0.012017721825904814 0.21013405969456617