BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779401.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 = 16,238,542 number of mapped reads = 15,495,830 (95.43%) number of supplementary alignments = 51,248 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,798,329 number of mapped paired reads (second in pair) = 7,697,501 number of mapped paired reads (both in pair) = 15,349,396 number of mapped paired reads (singletons) = 146,434 number of mapped bases = 1,231,700,140 bp number of sequenced bases = 1,231,413,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 509,975 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 38,214.9326 std insert size = 1,825,060.0848 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.3452 >>>>>>> ACTG content number of A's = 367,118,189 bp (29.81%) number of C's = 246,661,863 bp (20.03%) number of T's = 365,767,967 bp (29.7%) number of G's = 251,594,322 bp (20.43%) number of N's = 271,024 bp (0.02%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 4,262,723 number of insertions = 115,895 mapped reads with insertion percentage = 0.74% number of deletions = 137,116 mapped reads with deletion percentage = 0.87% homopolymer indels = 47.12% >>>>>>> Coverage mean coverageData = 0.3979X std coverageData = 1.612X There is a 19.85% of reference with a coverageData >= 1X There is a 9.15% of reference with a coverageData >= 2X There is a 4.58% of reference with a coverageData >= 3X There is a 2.46% of reference with a coverageData >= 4X There is a 1.37% of reference with a coverageData >= 5X There is a 0.79% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% 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 0.01% 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% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% 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 72784070 0.2920115894114462 2.945897188198859 chr2 243199373 89170500 0.3666559617322698 1.1295246012690976 chr3 198022430 53104065 0.2681719692057107 0.8072629716604292 chr4 191154276 88212506 0.4614728367363333 1.0902340755930453 chr5 180915260 115979643 0.6410716431549224 1.2810184168622012 chr6 171115067 37419552 0.2186806378657468 0.8040959302147224 chr7 159138663 169371859 1.0643036444261191 2.318973804224121 chr8 146364022 88140202 0.602198551225929 1.3144780949903068 chr9 141213431 52748172 0.3735350924233262 1.3213904984050775 chr10 135534747 29350189 0.21655102953045688 3.2897395282498536 chr11 135006516 65873641 0.48792934557321666 1.2560164167522967 chr12 133851895 36893509 0.27562933643935333 0.8566160378223223 chr13 115169878 47496024 0.41239970749990723 1.1177750487967615 chr14 107349540 31278667 0.291372156788003 0.8910833679573676 chr15 102531392 33660369 0.3282932996754789 0.9725286739911164 chr16 90354753 36128212 0.39984849496517355 1.1363185124943505 chr17 81195210 33813568 0.41644781754982835 1.2117246815640195 chr18 78077248 32166686 0.41198539682136337 1.4577042391018837 chr19 59128983 17055085 0.28843866636434456 3.007253192097089 chr20 63025520 29124074 0.46209970183506616 1.1383556009613909 chr21 48129895 19816975 0.4117394189204028 1.151668015110043 chr22 51304566 8827517 0.17206104033703354 0.6472356412325062 chrMT 16571 1190 0.07181220203970792 0.4462912483075353 chrX 155270560 39841519 0.25659416054144457 0.8532390263524403 chrY 59373566 3442346 0.05797775393851196 0.3743820139206538