BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779197.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 = 11,108,294 number of mapped reads = 10,805,296 (97.27%) number of supplementary alignments = 27,563 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,450,518 number of mapped paired reads (second in pair) = 5,354,778 number of mapped paired reads (both in pair) = 10,694,978 number of mapped paired reads (singletons) = 110,318 number of mapped bases = 859,958,678 bp number of sequenced bases = 859,797,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,330 duplication rate = 1.29% >>>>>>> Insert size mean insert size = 45,110.8769 std insert size = 1,945,830.3516 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 52.895 >>>>>>> ACTG content number of A's = 262,542,575 bp (30.54%) number of C's = 166,292,943 bp (19.34%) number of T's = 261,897,412 bp (30.46%) number of G's = 168,902,943 bp (19.64%) number of N's = 162,014 bp (0.02%) GC percentage = 38.99% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 3,301,000 number of insertions = 62,443 mapped reads with insertion percentage = 0.57% number of deletions = 77,690 mapped reads with deletion percentage = 0.71% homopolymer indels = 46.97% >>>>>>> Coverage mean coverageData = 0.2778X std coverageData = 0.8687X There is a 16.63% of reference with a coverageData >= 1X There is a 5.92% of reference with a coverageData >= 2X There is a 2.46% of reference with a coverageData >= 3X There is a 1.15% of reference with a coverageData >= 4X There is a 0.59% of reference with a coverageData >= 5X There is a 0.33% 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 0.05% 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 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 47472178 0.1904596177515642 0.6768901771902953 chr2 243199373 52078927 0.21414087691747463 0.6677359665106912 chr3 198022430 62817483 0.3172240791106341 0.8172091454466105 chr4 191154276 41917166 0.2192844799349401 0.6817188550327533 chr5 180915260 55486145 0.30669687565327547 0.8285233845381929 chr6 171115067 46852047 0.2738043342495375 0.8088943320022605 chr7 159138663 111910039 0.7032234460836208 1.7418401047725072 chr8 146364022 55029710 0.3759783944718327 0.8924352265494369 chr9 141213431 41310309 0.29253810142181164 0.8393206601758695 chr10 135534747 19164330 0.14139791030856463 1.0983885243860392 chr11 135006516 42276813 0.31314646324181866 0.8335149569093766 chr12 133851895 53879729 0.4025324333286428 0.9403459581323912 chr13 115169878 32946163 0.28606579751695144 0.7936859292646836 chr14 107349540 33520476 0.31225542279920343 0.9034623807472509 chr15 102531392 22628689 0.22070010519314903 0.6967717500451253 chr16 90354753 11377334 0.12591848931289756 0.48331751194897926 chr17 81195210 16557602 0.20392338415037045 0.6304680053498549 chr18 78077248 15944426 0.20421347330274756 0.6991103209962659 chr19 59128983 10442684 0.17660855083538304 0.616844359001543 chr20 63025520 21782060 0.34560698586858146 0.8613837615323284 chr21 48129895 8285069 0.17213976884844648 0.630404452080075 chr22 51304566 4155573 0.0809981123317562 0.36660459821248875 chrMT 16571 408 0.024621326413614145 0.20138512933520095 chrX 155270560 51602020 0.33233614923524457 0.92575596819729 chrY 59373566 521298 0.008779967839560117 0.14555079805545268