BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779078.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 = 29,501,420 number of mapped reads = 28,522,693 (96.68%) number of supplementary alignments = 168,335 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,406,147 number of mapped paired reads (second in pair) = 14,116,546 number of mapped paired reads (both in pair) = 28,125,140 number of mapped paired reads (singletons) = 397,553 number of mapped bases = 2,845,658,962 bp number of sequenced bases = 2,845,001,719 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,215,574 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 70,745.9658 std insert size = 2,582,604.9057 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 53.5426 >>>>>>> ACTG content number of A's = 864,236,528 bp (30.38%) number of C's = 555,963,721 bp (19.54%) number of T's = 858,346,498 bp (30.17%) number of G's = 565,511,114 bp (19.88%) number of N's = 943,858 bp (0.03%) GC percentage = 39.42% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 13,076,637 number of insertions = 239,941 mapped reads with insertion percentage = 0.83% number of deletions = 292,411 mapped reads with deletion percentage = 1.01% homopolymer indels = 46.3% >>>>>>> Coverage mean coverageData = 0.9192X std coverageData = 2.739X There is a 33.59% of reference with a coverageData >= 1X There is a 19.5% of reference with a coverageData >= 2X There is a 11.75% of reference with a coverageData >= 3X There is a 7.51% of reference with a coverageData >= 4X There is a 4.97% of reference with a coverageData >= 5X There is a 3.38% of reference with a coverageData >= 6X There is a 2.36% of reference with a coverageData >= 7X There is a 1.68% of reference with a coverageData >= 8X There is a 1.22% of reference with a coverageData >= 9X There is a 0.9% of reference with a coverageData >= 10X There is a 0.68% of reference with a coverageData >= 11X There is a 0.52% of reference with a coverageData >= 12X There is a 0.4% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 196270707 0.7874432015958749 2.2700910638329197 chr2 243199373 239791614 0.9859877969339995 2.3222256155227954 chr3 198022430 268445858 1.355633591608789 2.454635544271382 chr4 191154276 166723782 0.872194886187113 1.8792002641492267 chr5 180915260 123889919 0.6847952958749859 1.5978111979418337 chr6 171115067 220065104 1.2860650313160324 2.411711342257607 chr7 159138663 262012397 1.6464408589382205 7.555906562192651 chr8 146364022 211090825 1.442231650343689 2.503242359615349 chr9 141213431 106115793 0.751456800167967 2.120633363748799 chr10 135534747 40590021 0.2994805531307776 3.515677907372766 chr11 135006516 150437840 1.114300586795381 2.2627112944727585 chr12 133851895 144252661 1.077703539423181 2.1495746808441294 chr13 115169878 91618303 0.79550577452205 1.7292938812401708 chr14 107349540 123228414 1.147917485254245 2.273115542566729 chr15 102531392 69115316 0.6740893169576787 1.7100444547508378 chr16 90354753 73454581 0.812957576232874 1.8589409634958944 chr17 81195210 46075876 0.5674703717128141 1.5821315320137428 chr18 78077248 75312965 0.9645955374861573 2.131665402947179 chr19 59128983 35473883 0.5999406923673962 2.039141461846554 chr20 63025520 84115149 1.3346204680262852 2.6463802992795236 chr21 48129895 28251384 0.5869820409955184 1.5540333873738532 chr22 51304566 22221612 0.43313127334514434 1.2021452691558765 chrMT 16571 4674 0.28205901876772677 0.7174787262850867 chrX 155270560 65570078 0.4222956238452415 1.411186035557824 chrY 59373566 1530206 0.025772512973197534 0.4894173367395214