BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779370.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 = 16,477,826 number of mapped reads = 16,018,077 (97.21%) number of supplementary alignments = 89,609 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,040,254 number of mapped paired reads (second in pair) = 7,977,823 number of mapped paired reads (both in pair) = 15,922,560 number of mapped paired reads (singletons) = 95,517 number of mapped bases = 1,269,748,533 bp number of sequenced bases = 1,269,457,722 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 685,445 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 62,689.6268 std insert size = 2,371,055.5022 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 52.7967 >>>>>>> ACTG content number of A's = 385,580,494 bp (30.37%) number of C's = 248,656,347 bp (19.59%) number of T's = 382,580,160 bp (30.14%) number of G's = 252,360,728 bp (19.88%) number of N's = 279,993 bp (0.02%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 4,122,757 number of insertions = 141,891 mapped reads with insertion percentage = 0.88% number of deletions = 139,672 mapped reads with deletion percentage = 0.86% homopolymer indels = 47.12% >>>>>>> Coverage mean coverageData = 0.4102X std coverageData = 1.9257X There is a 18.21% of reference with a coverageData >= 1X There is a 9.39% of reference with a coverageData >= 2X There is a 4.94% of reference with a coverageData >= 3X There is a 2.86% of reference with a coverageData >= 4X There is a 1.72% of reference with a coverageData >= 5X There is a 1.08% of reference with a coverageData >= 6X There is a 0.7% of reference with a coverageData >= 7X There is a 0.46% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% 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 0.01% 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% 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 94993085 0.3811147375235627 4.123899786125566 chr2 243199373 97811079 0.40218474987597935 1.296718487321161 chr3 198022430 91695065 0.46305393282973045 1.244042825292536 chr4 191154276 96187295 0.5031919610315178 1.3181383436697154 chr5 180915260 128217743 0.7087171253547103 1.5242314779073143 chr6 171115067 60647207 0.3544235353629029 1.5076887087019233 chr7 159138663 134117724 0.8427727207938149 2.853711753355377 chr8 146364022 64437587 0.4402556456121437 1.2637114125319704 chr9 141213431 56324336 0.3988596240537488 1.8050245888254595 chr10 135534747 33734659 0.24890044617119475 2.8278977985873444 chr11 135006516 55999169 0.41478863879429345 1.3898390400796512 chr12 133851895 62357764 0.4658713572938209 1.2670590183550852 chr13 115169878 46875052 0.40700791573296624 1.1557382268145069 chr14 107349540 32200231 0.2999568605510559 1.0223333737991889 chr15 102531392 25492121 0.24862747401303203 0.8645830367345976 chr16 90354753 25210916 0.2790214699607446 1.0251076568599597 chr17 81195210 20699426 0.25493407800780366 1.3607199396282756 chr18 78077248 33852336 0.43357491288627387 2.0048940822033208 chr19 59128983 13345327 0.22569857154485476 2.857738336219952 chr20 63025520 23479359 0.3725373309097648 1.1455922488670593 chr21 48129895 18603312 0.38652301236061287 1.1839943977081153 chr22 51304566 7406177 0.14435707340356413 0.7152221802360729 chrMT 16571 2571 0.1551505642387303 0.5046466782109578 chrX 155270560 40443888 0.260473640334652 1.0802118139200259 chrY 59373566 5615104 0.09457245670573332 0.5276994080063103