BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779085.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 = 31,641,044 number of mapped reads = 29,330,060 (92.7%) number of supplementary alignments = 195,374 (0.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,918,816 number of mapped paired reads (second in pair) = 14,411,244 number of mapped paired reads (both in pair) = 28,650,584 number of mapped paired reads (singletons) = 679,476 number of mapped bases = 2,926,404,015 bp number of sequenced bases = 2,925,664,379 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 923,228 duplication rate = 2.32% >>>>>>> Insert size mean insert size = 55,788.3977 std insert size = 2,284,034.1497 median insert size = 302 >>>>>>> Mapping quality mean mapping quality = 53.8842 >>>>>>> ACTG content number of A's = 884,496,723 bp (30.23%) number of C's = 573,253,527 bp (19.59%) number of T's = 878,508,139 bp (30.03%) number of G's = 588,448,805 bp (20.11%) number of N's = 957,185 bp (0.03%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 16,921,593 number of insertions = 291,690 mapped reads with insertion percentage = 0.98% number of deletions = 334,000 mapped reads with deletion percentage = 1.12% homopolymer indels = 47.31% >>>>>>> Coverage mean coverageData = 0.9453X std coverageData = 3.4954X There is a 45.25% of reference with a coverageData >= 1X There is a 22.83% of reference with a coverageData >= 2X There is a 11.47% of reference with a coverageData >= 3X There is a 5.81% of reference with a coverageData >= 4X There is a 2.99% of reference with a coverageData >= 5X There is a 1.58% of reference with a coverageData >= 6X There is a 0.86% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% 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 0.03% 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 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% 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 219555995 0.8808643850881318 7.824790002517151 chr2 243199373 223941635 0.9208150178906916 2.205388140718645 chr3 198022430 186261604 0.9406086169127407 1.3909865331189344 chr4 191154276 172479341 0.9023043826652353 1.5081760901751025 chr5 180915260 187562186 1.036740549138862 1.4723995959874352 chr6 171115067 164230010 0.9597635841150096 1.7036445391890531 chr7 159138663 285773640 1.7957524250407961 6.891643166397291 chr8 146364022 212395026 1.4511423169281314 1.9308582903892244 chr9 141213431 112919321 0.7996358434205879 2.367686813078994 chr10 135534747 76416002 0.5638111531650256 6.5379375944243145 chr11 135006516 137276525 1.0168140699223733 1.5529530456634724 chr12 133851895 126229490 0.9430534397738635 1.5444977720361273 chr13 115169878 88768988 0.7707656684328519 1.334028139836651 chr14 107349540 97202156 0.9054734282047227 1.466648672501604 chr15 102531392 70145129 0.6841331969822472 1.3689147550755456 chr16 90354753 72382830 0.8010959866162215 1.4079768532574601 chr17 81195210 66749986 0.8220926579289591 2.4197591330363255 chr18 78077248 82020443 1.050503765194183 2.5825203193585353 chr19 59128983 49024204 0.8291061593262986 5.05060220941973 chr20 63025520 73290266 1.162866502331119 1.6953848397450386 chr21 48129895 42323588 0.8793617355699612 1.5429095684975977 chr22 51304566 25378110 0.49465597272570244 1.0889914754887073 chrMT 16571 4663 0.28139520849677147 0.6438981657205352 chrX 155270560 151959680 0.9786767047146606 1.6012272574137367 chrY 59373566 2113197 0.03559154590782033 0.4926669699728782