BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779278.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 = 14,226,620 number of mapped reads = 13,710,031 (96.37%) number of supplementary alignments = 31,171 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,913,920 number of mapped paired reads (second in pair) = 6,796,111 number of mapped paired reads (both in pair) = 13,568,362 number of mapped paired reads (singletons) = 141,669 number of mapped bases = 1,090,959,474 bp number of sequenced bases = 1,090,750,413 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 276,185 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 40,387.4012 std insert size = 1,869,907.9417 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 52.9723 >>>>>>> ACTG content number of A's = 332,517,030 bp (30.49%) number of C's = 211,551,850 bp (19.4%) number of T's = 331,256,658 bp (30.37%) number of G's = 215,216,531 bp (19.73%) number of N's = 208,344 bp (0.02%) GC percentage = 39.13% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 4,172,959 number of insertions = 79,570 mapped reads with insertion percentage = 0.57% number of deletions = 100,746 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.19% >>>>>>> Coverage mean coverageData = 0.3524X std coverageData = 1.26X There is a 19.96% of reference with a coverageData >= 1X There is a 7.8% of reference with a coverageData >= 2X There is a 3.35% of reference with a coverageData >= 3X There is a 1.59% of reference with a coverageData >= 4X There is a 0.8% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% 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 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% 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% 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 66709357 0.2676396822297185 2.0091794726403758 chr2 243199373 64719182 0.26611574364544105 0.7678763319696584 chr3 198022430 103758384 0.5239728852938528 1.0929734760824248 chr4 191154276 60516269 0.3165833915219349 0.8197913509832043 chr5 180915260 94689132 0.5233894144695146 1.0851888931708644 chr6 171115067 72491661 0.42364277016003504 1.038293518964072 chr7 159138663 90406851 0.5681011094079633 2.8367677190010188 chr8 146364022 80932465 0.5529532729019977 1.1505430457294692 chr9 141213431 37563898 0.2660079691711478 0.8259170092668522 chr10 135534747 15318961 0.11302607884013684 1.6463976364724793 chr11 135006516 61411611 0.4548788667355878 1.025474880929514 chr12 133851895 45222492 0.33785470127262673 0.8707068678382367 chr13 115169878 46154458 0.4007511234838679 0.9734906480163569 chr14 107349540 30454352 0.28369336282204843 0.8041599987530521 chr15 102531392 23643396 0.2305966547298997 0.7166581058924538 chr16 90354753 19383567 0.21452736415537543 0.6860910404238504 chr17 81195210 12201992 0.1502797024602806 0.5384186255876007 chr18 78077248 30243678 0.3873558402058433 0.9833549328392195 chr19 59128983 17269778 0.2920695930116031 1.3398411006882618 chr20 63025520 32704354 0.5189065318302808 1.1373189898185818 chr21 48129895 17339550 0.3602656934946565 0.9410813474530593 chr22 51304566 7245500 0.1412252468912806 0.5296310948724784 chrMT 16571 1225 0.0739243256291111 0.34202049043499805 chrX 155270560 59614321 0.38393833963115737 0.9581998908104387 chrY 59373566 963040 0.016220012791551042 0.24134236643334753