BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779196.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 11,942,624 number of mapped reads = 11,642,873 (97.49%) number of supplementary alignments = 29,053 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,851,298 number of mapped paired reads (second in pair) = 5,791,575 number of mapped paired reads (both in pair) = 11,567,668 number of mapped paired reads (singletons) = 75,205 number of mapped bases = 926,706,342 bp number of sequenced bases = 926,533,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 152,132 duplication rate = 1.19% >>>>>>> Insert size mean insert size = 44,997.8157 std insert size = 1,983,977.3046 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.9336 >>>>>>> ACTG content number of A's = 283,492,269 bp (30.6%) number of C's = 178,968,740 bp (19.32%) number of T's = 281,981,044 bp (30.43%) number of G's = 181,917,020 bp (19.63%) number of N's = 174,072 bp (0.02%) GC percentage = 38.95% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 3,522,068 number of insertions = 67,065 mapped reads with insertion percentage = 0.57% number of deletions = 84,150 mapped reads with deletion percentage = 0.71% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.2994X std coverageData = 0.8961X There is a 18.61% of reference with a coverageData >= 1X There is a 6.41% of reference with a coverageData >= 2X There is a 2.46% of reference with a coverageData >= 3X There is a 1.06% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 83623319 0.33549893943895126 0.998729298413783 chr2 243199373 58524374 0.24064360560666412 0.675942489793108 chr3 198022430 53719043 0.271277566889771 0.7240657946669973 chr4 191154276 67855571 0.3549780440171791 0.8246530146473926 chr5 180915260 56433117 0.31193121575261257 0.7601845998157617 chr6 171115067 68313374 0.39922477428594877 0.8915829243862312 chr7 159138663 89170302 0.5603308480730418 1.8841314613773439 chr8 146364022 72855834 0.49777146736238226 1.0203439836473813 chr9 141213431 27817823 0.19699134000929416 0.6287232455753552 chr10 135534747 27753363 0.20476935704170385 1.1398739020171327 chr11 135006516 32747350 0.24256125533970524 0.6889058118835266 chr12 133851895 49779946 0.3719031844861068 0.875301738211273 chr13 115169878 22120426 0.19206780786899852 0.5905502654937282 chr14 107349540 23081602 0.21501351566108248 0.6311837274729849 chr15 102531392 20071452 0.19575909005507308 0.6128296349820087 chr16 90354753 15973871 0.17679060004734892 0.5470557238750148 chr17 81195210 14514130 0.17875598819191427 0.6116407429789776 chr18 78077248 26587338 0.34052606464818025 0.8250977507202835 chr19 59128983 10743363 0.18169368818672224 0.6600513553731364 chr20 63025520 14942701 0.23708969001763094 0.6701304867265631 chr21 48129895 8672459 0.1801886125037256 0.5773477377160784 chr22 51304566 5983305 0.11662324558013024 0.4736009012765261 chrMT 16571 732 0.04417355621266067 0.3024316550419547 chrX 155270560 74787623 0.48166003265525675 1.0693289264828498 chrY 59373566 633924 0.01067687260017362 0.1427147536148643