BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781809.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 134,520,120 number of mapped reads = 132,332,390 (98.37%) number of supplementary alignments = 506,220 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 66,514,686 number of mapped paired reads (second in pair) = 65,817,704 number of mapped paired reads (both in pair) = 131,167,722 number of mapped paired reads (singletons) = 1,164,668 number of mapped bases = 13,145,051,377 bp number of sequenced bases = 13,142,282,507 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,325,118 duplication rate = 5.28% >>>>>>> Insert size mean insert size = 42,344.3012 std insert size = 2,006,370.9307 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.0492 >>>>>>> ACTG content number of A's = 3,875,900,033 bp (29.49%) number of C's = 2,683,301,645 bp (20.42%) number of T's = 3,850,176,283 bp (29.3%) number of G's = 2,731,824,254 bp (20.79%) number of N's = 1,080,292 bp (0.01%) GC percentage = 41.2% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 52,905,292 number of insertions = 1,252,660 mapped reads with insertion percentage = 0.93% number of deletions = 1,232,474 mapped reads with deletion percentage = 0.91% homopolymer indels = 46.35% >>>>>>> Coverage mean coverageData = 4.2462X std coverageData = 5.5372X There is a 80.53% of reference with a coverageData >= 1X There is a 67.99% of reference with a coverageData >= 2X There is a 55.64% of reference with a coverageData >= 3X There is a 44.68% of reference with a coverageData >= 4X There is a 35.47% of reference with a coverageData >= 5X There is a 27.98% of reference with a coverageData >= 6X There is a 22.02% of reference with a coverageData >= 7X There is a 17.34% of reference with a coverageData >= 8X There is a 13.68% of reference with a coverageData >= 9X There is a 10.82% of reference with a coverageData >= 10X There is a 8.59% of reference with a coverageData >= 11X There is a 6.85% of reference with a coverageData >= 12X There is a 5.49% of reference with a coverageData >= 13X There is a 4.42% of reference with a coverageData >= 14X There is a 3.58% of reference with a coverageData >= 15X There is a 2.91% of reference with a coverageData >= 16X There is a 2.38% of reference with a coverageData >= 17X There is a 1.96% of reference with a coverageData >= 18X There is a 1.62% of reference with a coverageData >= 19X There is a 1.34% of reference with a coverageData >= 20X There is a 1.12% of reference with a coverageData >= 21X There is a 0.94% of reference with a coverageData >= 22X There is a 0.79% of reference with a coverageData >= 23X There is a 0.67% of reference with a coverageData >= 24X There is a 0.57% of reference with a coverageData >= 25X There is a 0.49% of reference with a coverageData >= 26X There is a 0.42% of reference with a coverageData >= 27X There is a 0.36% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1062632877 4.26331085048731 8.071917393181563 chr2 243199373 1106958872 4.551651833411594 5.39184336620221 chr3 198022430 904778304 4.569069796790192 4.576011067082264 chr4 191154276 846920404 4.43055955494294 5.227112676227542 chr5 180915260 804001097 4.444075624134747 4.3990944097006 chr6 171115067 769450759 4.4966861918711105 5.097384918236568 chr7 159138663 683820845 4.297012631053712 5.050478362907298 chr8 146364022 664775318 4.541931199458293 4.748800185887313 chr9 141213431 551870739 3.9080612594137736 5.622058625884963 chr10 135534747 746901158 5.510772510609401 8.182905206218578 chr11 135006516 612483263 4.536694088157938 4.970572843967594 chr12 133851895 592832586 4.429018998946559 4.717372062641996 chr13 115169878 410609302 3.5652490836188955 4.1387859825540465 chr14 107349540 399675416 3.723121831728389 4.473383397493848 chr15 102531392 374618066 3.6536914079933687 4.5091726605049285 chr16 90354753 336172598 3.7205856564070294 4.64353062134941 chr17 81195210 307872994 3.7917630116357848 5.130543143858922 chr18 78077248 344766032 4.415704201049709 5.79642652246171 chr19 59128983 211308414 3.573685919813639 5.806160706351797 chr20 63025520 266069751 4.221619290090744 5.183108761196816 chr21 48129895 159107328 3.305790050030236 7.256528898130605 chr22 51304566 128390666 2.5025192884391614 4.0266517806354525 chrMT 16571 349746 21.105907911411503 6.37864766960304 chrX 155270560 846165966 5.449622684429038 5.582610402140224 chrY 59373566 12518876 0.21084931971241208 2.4423442614082895