BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779314.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 = 17,763,222 number of mapped reads = 17,126,618 (96.42%) number of supplementary alignments = 42,397 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,624,953 number of mapped paired reads (second in pair) = 8,501,665 number of mapped paired reads (both in pair) = 16,976,558 number of mapped paired reads (singletons) = 150,060 number of mapped bases = 1,363,631,422 bp number of sequenced bases = 1,363,374,911 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 604,838 duplication rate = 3.32% >>>>>>> Insert size mean insert size = 41,922.2937 std insert size = 1,929,795.4401 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.8664 >>>>>>> ACTG content number of A's = 421,011,571 bp (30.88%) number of C's = 258,798,457 bp (18.98%) number of T's = 420,421,136 bp (30.84%) number of G's = 262,782,161 bp (19.27%) number of N's = 361,586 bp (0.03%) GC percentage = 38.26% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 4,787,920 number of insertions = 98,043 mapped reads with insertion percentage = 0.57% number of deletions = 125,544 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.99% >>>>>>> Coverage mean coverageData = 0.4405X std coverageData = 1.6698X There is a 16.59% of reference with a coverageData >= 1X There is a 8.62% of reference with a coverageData >= 2X There is a 5.22% of reference with a coverageData >= 3X There is a 3.43% of reference with a coverageData >= 4X There is a 2.37% of reference with a coverageData >= 5X There is a 1.7% of reference with a coverageData >= 6X There is a 1.25% of reference with a coverageData >= 7X There is a 0.94% of reference with a coverageData >= 8X There is a 0.72% of reference with a coverageData >= 9X There is a 0.56% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% 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% 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 113100320 0.45376143716809436 2.142515577087407 chr2 243199373 150290658 0.6179730488038717 1.845310541756464 chr3 198022430 85882909 0.433702934561504 1.4605881209021403 chr4 191154276 99766517 0.5219162191276328 1.6750138195783713 chr5 180915260 100944283 0.5579644470013199 1.754431219192176 chr6 171115067 74074248 0.43289144140650104 1.4694744917827727 chr7 159138663 96517406 0.6064987865331004 2.1340888383993786 chr8 146364022 103602387 0.7078405306462541 1.977663085564884 chr9 141213431 51498262 0.3646838805297493 1.4099479837089481 chr10 135534747 28787969 0.21240286817372375 1.6427086403707167 chr11 135006516 68388618 0.5065579056939741 1.8384947474957278 chr12 133851895 58995943 0.4407553811621419 1.6302375089211063 chr13 115169878 41176875 0.35753163687470435 1.333612076469294 chr14 107349540 44050649 0.4103478133208582 1.5219357740579635 chr15 102531392 31848900 0.3106258422786262 1.4254517840092082 chr16 90354753 22288725 0.2466801608101347 1.131517545870498 chr17 81195210 12494970 0.15388801876366845 0.8363274214465309 chr18 78077248 38906232 0.49830434597284984 1.6599686860922613 chr19 59128983 7623465 0.12892941182499282 0.9639147043980956 chr20 63025520 25375441 0.402621684041639 1.287788244849121 chr21 48129895 9850429 0.20466342176728206 0.8950140065780137 chr22 51304566 6109769 0.11908821136894521 0.6450440203365514 chrMT 16571 3259 0.19666887936756985 0.46072266150311153 chrX 155270560 91203881 0.58738682336175 2.0794068042113674 chrY 59373566 849307 0.014304463370113225 0.19172682582466885