BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976565.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 = 779,966,256 number of mapped reads = 767,380,905 (98.39%) number of supplementary alignments = 2,361,952 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 385,289,964 number of mapped paired reads (second in pair) = 382,090,941 number of mapped paired reads (both in pair) = 762,010,106 number of mapped paired reads (singletons) = 5,370,799 number of mapped bases = 109,776,077,063 bp number of sequenced bases = 109,738,701,292 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,781,791 duplication rate = 15.07% >>>>>>> Insert size mean insert size = 23,087.1423 std insert size = 1,437,641.8311 median insert size = 394 >>>>>>> Mapping quality mean mapping quality = 54.4388 >>>>>>> ACTG content number of A's = 32,198,518,958 bp (29.34%) number of C's = 22,566,679,125 bp (20.56%) number of T's = 32,367,247,009 bp (29.49%) number of G's = 22,603,747,645 bp (20.6%) number of N's = 2,508,555 bp (0%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 879,005,084 number of insertions = 11,711,065 mapped reads with insertion percentage = 1.43% number of deletions = 13,378,507 mapped reads with deletion percentage = 1.66% homopolymer indels = 42.27% >>>>>>> Coverage mean coverageData = 35.4609X std coverageData = 355.4756X There is a 92.29% of reference with a coverageData >= 1X There is a 92.25% of reference with a coverageData >= 2X There is a 92.21% of reference with a coverageData >= 3X There is a 92.17% of reference with a coverageData >= 4X There is a 92.12% of reference with a coverageData >= 5X There is a 92.07% of reference with a coverageData >= 6X There is a 92% of reference with a coverageData >= 7X There is a 91.92% of reference with a coverageData >= 8X There is a 91.81% of reference with a coverageData >= 9X There is a 91.67% of reference with a coverageData >= 10X There is a 91.5% of reference with a coverageData >= 11X There is a 91.26% of reference with a coverageData >= 12X There is a 90.97% of reference with a coverageData >= 13X There is a 90.6% of reference with a coverageData >= 14X There is a 90.14% of reference with a coverageData >= 15X There is a 89.61% of reference with a coverageData >= 16X There is a 88.99% of reference with a coverageData >= 17X There is a 88.28% of reference with a coverageData >= 18X There is a 87.51% of reference with a coverageData >= 19X There is a 86.67% of reference with a coverageData >= 20X There is a 85.77% of reference with a coverageData >= 21X There is a 84.8% of reference with a coverageData >= 22X There is a 83.75% of reference with a coverageData >= 23X There is a 82.62% of reference with a coverageData >= 24X There is a 81.37% of reference with a coverageData >= 25X There is a 79.98% of reference with a coverageData >= 26X There is a 78.42% of reference with a coverageData >= 27X There is a 76.64% of reference with a coverageData >= 28X There is a 74.62% of reference with a coverageData >= 29X There is a 72.33% of reference with a coverageData >= 30X There is a 69.75% of reference with a coverageData >= 31X There is a 66.86% of reference with a coverageData >= 32X There is a 63.67% of reference with a coverageData >= 33X There is a 60.19% of reference with a coverageData >= 34X There is a 56.46% of reference with a coverageData >= 35X There is a 52.51% of reference with a coverageData >= 36X There is a 48.4% of reference with a coverageData >= 37X There is a 44.2% of reference with a coverageData >= 38X There is a 39.96% of reference with a coverageData >= 39X There is a 35.77% of reference with a coverageData >= 40X There is a 31.69% of reference with a coverageData >= 41X There is a 27.79% of reference with a coverageData >= 42X There is a 24.11% of reference with a coverageData >= 43X There is a 20.7% of reference with a coverageData >= 44X There is a 17.59% of reference with a coverageData >= 45X There is a 14.8% of reference with a coverageData >= 46X There is a 12.34% of reference with a coverageData >= 47X There is a 10.2% of reference with a coverageData >= 48X There is a 8.36% of reference with a coverageData >= 49X There is a 6.81% of reference with a coverageData >= 50X There is a 5.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9085140218 36.44981979001769 832.4670449977366 chr2 243199373 9507661118 39.09410209704776 211.8845293400853 chr3 198022430 7324820576 36.98985299796594 18.475697806346826 chr4 191154276 7303162963 38.20559558395649 248.670687645268 chr5 180915260 6690821859 36.98318129161686 32.787656955218836 chr6 171115067 6382047723 37.29681923918482 148.8603208726786 chr7 159138663 6038592111 37.94547470214702 364.265113716979 chr8 146364022 5595645324 38.231016390079795 267.86276672519466 chr9 141213431 4857593125 34.398945557806044 662.9000761689263 chr10 135534747 5688667966 41.97202630259826 624.8408570798262 chr11 135006516 5083069100 37.650546437329 144.28421706018577 chr12 133851895 4901902651 36.62183976551098 21.15350752487484 chr13 115169878 3516105739 30.52973398999346 18.128216316251205 chr14 107349540 3336462152 31.08035816455292 25.170248599895377 chr15 102531392 3139495587 30.61984749997347 19.512866426203452 chr16 90354753 3456610238 38.25598679905638 208.37324694556824 chr17 81195210 3109770798 38.2999292445946 202.59687455414948 chr18 78077248 3139354738 40.208316999082754 506.02173017665666 chr19 59128983 2201184866 37.22683452884688 356.76850765877884 chr20 63025520 2346800409 37.23571672236897 60.451464366874625 chr21 48129895 1550941492 32.22407802884257 101.07614413152626 chr22 51304566 1365747587 26.620390610067727 66.62961275408483 chrMT 16571 156788597 9461.625550660792 1077.721134555297 chrX 155270560 2929517238 18.867177641402208 41.28239278397802 chrY 59373566 1068172888 17.990714723114323 274.74862270509414