BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779380.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 = 13,665,860 number of mapped reads = 12,989,894 (95.05%) number of supplementary alignments = 58,916 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,545,060 number of mapped paired reads (second in pair) = 6,444,834 number of mapped paired reads (both in pair) = 12,856,326 number of mapped paired reads (singletons) = 133,568 number of mapped bases = 1,032,386,914 bp number of sequenced bases = 1,032,145,171 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 870,388 duplication rate = 6.17% >>>>>>> Insert size mean insert size = 48,349.6406 std insert size = 2,093,346.2543 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 52.3062 >>>>>>> ACTG content number of A's = 311,475,849 bp (30.18%) number of C's = 203,117,020 bp (19.68%) number of T's = 310,327,053 bp (30.07%) number of G's = 206,995,443 bp (20.05%) number of N's = 229,806 bp (0.02%) GC percentage = 39.73% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 3,605,835 number of insertions = 100,265 mapped reads with insertion percentage = 0.76% number of deletions = 115,823 mapped reads with deletion percentage = 0.88% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.3335X std coverageData = 1.8924X There is a 10.02% of reference with a coverageData >= 1X There is a 5.51% of reference with a coverageData >= 2X There is a 3.6% of reference with a coverageData >= 3X There is a 2.58% of reference with a coverageData >= 4X There is a 1.93% of reference with a coverageData >= 5X There is a 1.5% of reference with a coverageData >= 6X There is a 1.19% of reference with a coverageData >= 7X There is a 0.96% of reference with a coverageData >= 8X There is a 0.79% of reference with a coverageData >= 9X There is a 0.66% of reference with a coverageData >= 10X There is a 0.55% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.4% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.15% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 77488448 0.3108856767903499 2.204922550035493 chr2 243199373 80238031 0.32992696490216694 1.6098893778492906 chr3 198022430 104220874 0.5263084287976872 2.4380180753151928 chr4 191154276 32308488 0.1690178670133437 0.9851562453775703 chr5 180915260 57142169 0.315850465018816 1.943697191992235 chr6 171115067 64540811 0.3771778378814532 1.9111156929212991 chr7 159138663 134266418 0.843707088327115 2.873291088877164 chr8 146364022 33360511 0.22792835660118715 1.5645469407860377 chr9 141213431 53133317 0.3762624887996667 1.9585256738534895 chr10 135534747 36728672 0.27099081831760824 2.35468743226611 chr11 135006516 49932484 0.36985240030933025 1.7084099950326095 chr12 133851895 23640201 0.17661461572882475 1.1999955372581101 chr13 115169878 47864312 0.4155974880862512 2.030206851751497 chr14 107349540 47506321 0.44253865456712715 2.2572443697000035 chr15 102531392 23306119 0.2273071548662872 1.2974925329637883 chr16 90354753 46801668 0.5179768240858342 2.5845761002897296 chr17 81195210 13497568 0.1662360131835363 1.2153340128792178 chr18 78077248 19757363 0.2530489163757411 1.7494860783740878 chr19 59128983 13377034 0.22623480603412374 1.9347643686590863 chr20 63025520 16692499 0.2648530150961071 1.4472781505043248 chr21 48129895 22746546 0.47260743037149777 1.9660190980174632 chr22 51304566 7347631 0.1432159274088782 1.1831182443512385 chrMT 16571 2178 0.1314344336491461 0.5260537931583138 chrX 155270560 23708742 0.1526930926248994 1.0060765250121415 chrY 59373566 2778509 0.046797071275793 0.47051904597766453