BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779080.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 = 26,301,926 number of mapped reads = 25,640,951 (97.49%) number of supplementary alignments = 136,763 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,920,080 number of mapped paired reads (second in pair) = 12,720,871 number of mapped paired reads (both in pair) = 25,356,090 number of mapped paired reads (singletons) = 284,861 number of mapped bases = 2,561,101,123 bp number of sequenced bases = 2,560,521,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 950,820 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 58,402.3698 std insert size = 2,291,464.8041 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.6424 >>>>>>> ACTG content number of A's = 780,339,320 bp (30.48%) number of C's = 497,694,381 bp (19.44%) number of T's = 775,955,581 bp (30.3%) number of G's = 505,684,876 bp (19.75%) number of N's = 847,036 bp (0.03%) GC percentage = 39.19% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 11,715,660 number of insertions = 211,203 mapped reads with insertion percentage = 0.81% number of deletions = 259,570 mapped reads with deletion percentage = 0.99% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.8273X std coverageData = 2.6126X There is a 34.84% of reference with a coverageData >= 1X There is a 18.74% of reference with a coverageData >= 2X There is a 10.33% of reference with a coverageData >= 3X There is a 6.02% of reference with a coverageData >= 4X There is a 3.64% of reference with a coverageData >= 5X There is a 2.28% of reference with a coverageData >= 6X There is a 1.47% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.67% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 178590242 0.7165087143353597 3.351588301790702 chr2 243199373 198740130 0.8171901413578069 1.7871397322572304 chr3 198022430 164197339 0.8291855574138748 1.5708898088144763 chr4 191154276 172115687 0.9004019716514214 1.663913157645804 chr5 180915260 157664297 0.871481471491128 1.6241047752961135 chr6 171115067 135403460 0.7913006281322965 1.6600380603941005 chr7 159138663 292828516 1.8400840529871738 7.626023039859321 chr8 146364022 195583821 1.33628345495999 2.119782662198194 chr9 141213431 104716243 0.7415459156997609 1.8318266553038764 chr10 135534747 52145569 0.38473948676792086 3.4442650416264513 chr11 135006516 88204257 0.6533333324444873 1.4019161497653394 chr12 133851895 124025308 0.9265861196810101 1.7402055438949398 chr13 115169878 99142433 0.8608364853872642 1.6906832405237286 chr14 107349540 73794088 0.6874187630426735 1.487496300852967 chr15 102531392 60739198 0.5923961122072741 1.4519284021047332 chr16 90354753 54113966 0.59890558275335 1.3494559505287718 chr17 81195210 40670575 0.5008986983345446 1.5168158606997182 chr18 78077248 74284379 0.9514215844287954 1.8568652533655259 chr19 59128983 23977421 0.405510458382144 1.923720474054988 chr20 63025520 52814422 0.8379847084165272 1.6701924317376708 chr21 48129895 34255927 0.7117390760981298 1.5409165741346114 chr22 51304566 16389255 0.3194502220328694 0.9507929075755793 chrMT 16571 21662 1.3072234626757588 1.2603545031576224 chrX 155270560 165143921 1.0635881071080056 2.0035665964919636 chrY 59373566 1539007 0.02592074392163004 0.3728143208544518