BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779231.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 = 8,470,910 number of mapped reads = 8,015,465 (94.62%) number of supplementary alignments = 18,749 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,077,657 number of mapped paired reads (second in pair) = 3,937,808 number of mapped paired reads (both in pair) = 7,863,234 number of mapped paired reads (singletons) = 152,231 number of mapped bases = 637,740,207 bp number of sequenced bases = 637,617,612 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,461 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 53,821.0172 std insert size = 2,216,733.2404 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 52.7841 >>>>>>> ACTG content number of A's = 195,812,706 bp (30.71%) number of C's = 122,012,298 bp (19.14%) number of T's = 195,420,511 bp (30.65%) number of G's = 124,254,188 bp (19.49%) number of N's = 117,909 bp (0.02%) GC percentage = 38.62% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 2,544,504 number of insertions = 46,664 mapped reads with insertion percentage = 0.58% number of deletions = 58,952 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 0.206X std coverageData = 0.8442X There is a 11.9% of reference with a coverageData >= 1X There is a 4.24% of reference with a coverageData >= 2X There is a 1.87% of reference with a coverageData >= 3X There is a 0.95% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 80463942 0.32282343641583144 1.1026393008601545 chr2 243199373 44088820 0.18128673382722907 0.6523918905040941 chr3 198022430 50002557 0.2525095616693523 0.7966702034845592 chr4 191154276 29206309 0.15278920048851014 0.5611101631784948 chr5 180915260 41046977 0.22688510079249258 0.736495627464591 chr6 171115067 47325713 0.27657244817605686 0.8541105497310235 chr7 159138663 62979379 0.3957515905484263 2.0265414313771184 chr8 146364022 39420268 0.2693303139756572 0.8218472150290506 chr9 141213431 24385923 0.1726884109203465 0.6714884182665823 chr10 135534747 9511529 0.07017778990652486 0.46359492580007083 chr11 135006516 30976218 0.22944239224720087 0.7842378467719858 chr12 133851895 19951294 0.14905499843689177 0.627696404718096 chr13 115169878 23444785 0.20356698649971652 0.6738869112380235 chr14 107349540 21582272 0.20104671151827944 0.7295475987899515 chr15 102531392 12298932 0.11995284332041449 0.5055875677626939 chr16 90354753 8005890 0.08860507869464267 0.39555321161311163 chr17 81195210 12604589 0.15523808608906856 0.6350156263026312 chr18 78077248 16527093 0.21167617229541696 0.7207357826891128 chr19 59128983 7965484 0.13471369869493613 0.6053241925967187 chr20 63025520 9136753 0.14496910140527203 0.5962085232777606 chr21 48129895 5983473 0.12431926144862772 0.5571267099183174 chr22 51304566 2071223 0.04037112408279606 0.2803184722395492 chrMT 16571 1619 0.09770080260696397 0.32541849045176535 chrX 155270560 38482711 0.24784293300674642 0.8068252827270762 chrY 59373566 276454 0.004656179822515629 0.09054533519543924