BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779282.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 = 8,575,604 number of mapped reads = 8,367,231 (97.57%) number of supplementary alignments = 18,243 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,215,710 number of mapped paired reads (second in pair) = 4,151,521 number of mapped paired reads (both in pair) = 8,292,232 number of mapped paired reads (singletons) = 74,999 number of mapped bases = 665,903,200 bp number of sequenced bases = 665,775,795 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,376 duplication rate = 0.85% >>>>>>> Insert size mean insert size = 43,535.1689 std insert size = 1,968,118.7683 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 53.1445 >>>>>>> ACTG content number of A's = 203,260,124 bp (30.53%) number of C's = 128,700,512 bp (19.33%) number of T's = 202,926,475 bp (30.48%) number of G's = 130,764,036 bp (19.64%) number of N's = 124,648 bp (0.02%) GC percentage = 38.97% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 2,622,944 number of insertions = 48,111 mapped reads with insertion percentage = 0.57% number of deletions = 61,156 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.42% >>>>>>> Coverage mean coverageData = 0.2151X std coverageData = 0.6773X There is a 15.38% of reference with a coverageData >= 1X There is a 4.08% of reference with a coverageData >= 2X There is a 1.18% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.15% 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 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 14X There is a 0.01% 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% 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 44232520 0.1774620252601096 0.8157033364353923 chr2 243199373 56382269 0.2318355853655922 0.600496058078601 chr3 198022430 51835122 0.261763892100506 0.6405892209132377 chr4 191154276 55362354 0.2896213213666222 0.6771229315982267 chr5 180915260 37658910 0.20815773086250436 0.5632044667945532 chr6 171115067 47629324 0.2783467571561071 0.6736184402083346 chr7 159138663 65571008 0.4120369416450357 1.3284014580023826 chr8 146364022 42550183 0.2907147700546245 0.6844618082659797 chr9 141213431 26813289 0.189877753200402 0.5676120474012509 chr10 135534747 14682503 0.10833017602489788 0.8019736663557496 chr11 135006516 25438950 0.18842757189586315 0.5413700014528297 chr12 133851895 26850613 0.2005994237137995 0.5522819765168132 chr13 115169878 21794972 0.1892419474474046 0.5381155934317686 chr14 107349540 22209519 0.20688974540552293 0.5782451396732634 chr15 102531392 12249867 0.11947430695176751 0.4309433169968577 chr16 90354753 12969912 0.1435443246687864 0.45753105442085695 chr17 81195210 12613413 0.1553467624506421 0.5211365726701529 chr18 78077248 14049715 0.17994633980951788 0.5340167412622163 chr19 59128983 8853666 0.1497347924959237 0.6123925785929719 chr20 63025520 13224743 0.2098315571216231 0.5788744588114242 chr21 48129895 7680044 0.159569099413161 0.5043382261075381 chr22 51304566 4023796 0.07842958850874988 0.34261934341299866 chrMT 16571 1037 0.06257920463460262 0.29906471841212035 chrX 155270560 40828935 0.262953485837882 0.6661069866457845 chrY 59373566 396536 0.0066786623528726574 0.10797670321613861