BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976566.sorted.bam outfile = /home/yangyx/scDNA/SRP067062/SRP067062.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 = 640,855,848 number of mapped reads = 631,956,424 (98.61%) number of supplementary alignments = 1,999,630 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 317,262,663 number of mapped paired reads (second in pair) = 314,693,761 number of mapped paired reads (both in pair) = 627,492,554 number of mapped paired reads (singletons) = 4,463,870 number of mapped bases = 90,303,933,735 bp number of sequenced bases = 90,273,112,872 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,556,499 duplication rate = 12.75% >>>>>>> Insert size mean insert size = 23,343.8629 std insert size = 1,445,066.4502 median insert size = 392 >>>>>>> Mapping quality mean mapping quality = 54.4137 >>>>>>> ACTG content number of A's = 26,520,071,251 bp (29.38%) number of C's = 18,550,173,254 bp (20.55%) number of T's = 26,657,490,319 bp (29.53%) number of G's = 18,543,334,691 bp (20.54%) number of N's = 2,043,357 bp (0%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 748,747,131 number of insertions = 9,685,627 mapped reads with insertion percentage = 1.44% number of deletions = 11,034,052 mapped reads with deletion percentage = 1.67% homopolymer indels = 42.14% >>>>>>> Coverage mean coverageData = 29.1708X std coverageData = 308.6545X There is a 92.28% of reference with a coverageData >= 1X There is a 92.23% of reference with a coverageData >= 2X There is a 92.18% of reference with a coverageData >= 3X There is a 92.11% of reference with a coverageData >= 4X There is a 92.04% of reference with a coverageData >= 5X There is a 91.94% of reference with a coverageData >= 6X There is a 91.82% of reference with a coverageData >= 7X There is a 91.64% of reference with a coverageData >= 8X There is a 91.4% of reference with a coverageData >= 9X There is a 91.08% of reference with a coverageData >= 10X There is a 90.67% of reference with a coverageData >= 11X There is a 90.14% of reference with a coverageData >= 12X There is a 89.49% of reference with a coverageData >= 13X There is a 88.73% of reference with a coverageData >= 14X There is a 87.85% of reference with a coverageData >= 15X There is a 86.85% of reference with a coverageData >= 16X There is a 85.75% of reference with a coverageData >= 17X There is a 84.52% of reference with a coverageData >= 18X There is a 83.17% of reference with a coverageData >= 19X There is a 81.65% of reference with a coverageData >= 20X There is a 79.92% of reference with a coverageData >= 21X There is a 77.95% of reference with a coverageData >= 22X There is a 75.68% of reference with a coverageData >= 23X There is a 73.08% of reference with a coverageData >= 24X There is a 70.1% of reference with a coverageData >= 25X There is a 66.74% of reference with a coverageData >= 26X There is a 62.99% of reference with a coverageData >= 27X There is a 58.88% of reference with a coverageData >= 28X There is a 54.47% of reference with a coverageData >= 29X There is a 49.83% of reference with a coverageData >= 30X There is a 45.04% of reference with a coverageData >= 31X There is a 40.22% of reference with a coverageData >= 32X There is a 35.45% of reference with a coverageData >= 33X There is a 30.85% of reference with a coverageData >= 34X There is a 26.48% of reference with a coverageData >= 35X There is a 22.44% of reference with a coverageData >= 36X There is a 18.77% of reference with a coverageData >= 37X There is a 15.5% of reference with a coverageData >= 38X There is a 12.65% of reference with a coverageData >= 39X There is a 10.21% of reference with a coverageData >= 40X There is a 8.16% of reference with a coverageData >= 41X There is a 6.47% of reference with a coverageData >= 42X There is a 5.1% of reference with a coverageData >= 43X There is a 4.01% of reference with a coverageData >= 44X There is a 3.15% of reference with a coverageData >= 45X There is a 2.49% of reference with a coverageData >= 46X There is a 1.99% of reference with a coverageData >= 47X There is a 1.61% of reference with a coverageData >= 48X There is a 1.32% of reference with a coverageData >= 49X There is a 1.12% of reference with a coverageData >= 50X There is a 0.96% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7450045562 29.889777333794488 723.6812606531329 chr2 243199373 7820383658 32.15626570714884 182.96412927046254 chr3 198022430 6013670113 30.36863103336324 15.476499464599971 chr4 191154276 6042865436 31.61250463473807 213.92484661701485 chr5 180915260 5504446297 30.425550044811036 27.58262686386993 chr6 171115067 5250716975 30.685298887210205 127.5067226886097 chr7 159138663 4967333232 31.213868071770843 313.71534905937824 chr8 146364022 4600922627 31.434792267460374 222.93281635695578 chr9 141213431 3992592473 28.273461275790403 571.3966256780677 chr10 135534747 4698516254 34.666506988056724 551.9227026203451 chr11 135006516 4166805723 30.86373788802905 121.06415035825454 chr12 133851895 4019527147 30.029661866199206 17.6027386704596 chr13 115169878 2900543323 25.184912699134753 15.10024657727958 chr14 107349540 2740042215 25.524489578623253 20.853342341667133 chr15 102531392 2567306223 25.039221383047252 16.141684703045478 chr16 90354753 2831885293 31.341851966547903 180.90934984814285 chr17 81195210 2533824661 31.206578085086548 176.40648918563173 chr18 78077248 2575593747 32.98776292678758 416.099380540274 chr19 59128983 1785117269 30.190224462341927 300.49899007449176 chr20 63025520 1909778104 30.301663580086288 51.35114923126198 chr21 48129895 1277337365 26.53937568324219 85.39476395977574 chr22 51304566 1106086215 21.559215899029336 61.9691454402599 chrMT 16571 236650648 14281.011888238489 1654.3392131781939 chrX 155270560 2411744118 15.532526694049407 36.46647884723517 chrY 59373566 900199057 15.161613452693746 237.35230799221677