BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779172.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 = 25,338,874 number of mapped reads = 24,599,435 (97.08%) number of supplementary alignments = 143,304 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,390,807 number of mapped paired reads (second in pair) = 12,208,628 number of mapped paired reads (both in pair) = 24,331,202 number of mapped paired reads (singletons) = 268,233 number of mapped bases = 2,457,619,673 bp number of sequenced bases = 2,457,091,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 881,975 duplication rate = 3.26% >>>>>>> Insert size mean insert size = 62,950.3027 std insert size = 2,390,085.6665 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 53.5607 >>>>>>> ACTG content number of A's = 751,729,938 bp (30.59%) number of C's = 474,603,003 bp (19.32%) number of T's = 748,501,205 bp (30.46%) number of G's = 481,260,410 bp (19.59%) number of N's = 996,664 bp (0.04%) GC percentage = 38.9% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 9,687,106 number of insertions = 196,413 mapped reads with insertion percentage = 0.79% number of deletions = 237,492 mapped reads with deletion percentage = 0.95% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.7939X std coverageData = 2.205X There is a 28.97% of reference with a coverageData >= 1X There is a 16.44% of reference with a coverageData >= 2X There is a 9.9% of reference with a coverageData >= 3X There is a 6.42% of reference with a coverageData >= 4X There is a 4.35% of reference with a coverageData >= 5X There is a 3.05% of reference with a coverageData >= 6X There is a 2.19% of reference with a coverageData >= 7X There is a 1.62% of reference with a coverageData >= 8X There is a 1.21% of reference with a coverageData >= 9X There is a 0.92% of reference with a coverageData >= 10X There is a 0.72% of reference with a coverageData >= 11X There is a 0.56% of reference with a coverageData >= 12X There is a 0.45% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.2% of reference with a coverageData >= 17X There is a 0.17% of reference with a coverageData >= 18X There is a 0.14% of reference with a coverageData >= 19X There is a 0.12% of reference with a coverageData >= 20X There is a 0.1% of reference with a coverageData >= 21X There is a 0.09% 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 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% 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 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 231354805 0.9282015189041395 2.505345952230661 chr2 243199373 158651892 0.6523532114533864 1.9799118226845438 chr3 198022430 179284355 0.9053739770792631 2.0309137708604954 chr4 191154276 198076274 1.0362115781286525 2.1924829212158126 chr5 180915260 178680839 0.9876493503090895 2.184644545800709 chr6 171115067 140973621 0.82385276452599 1.9223279278470213 chr7 159138663 227930053 1.4322732685016966 4.202484544636964 chr8 146364022 169885468 1.1607051082539943 2.4108401889360387 chr9 141213431 85362956 0.6044960128473899 1.6488421482670779 chr10 135534747 52275858 0.3857007826930167 2.376499886665984 chr11 135006516 112020973 0.8297449361629331 2.1071623983469077 chr12 133851895 123606487 0.9234571314810298 2.249670090106619 chr13 115169878 69446573 0.6029925029528989 1.5804436842076564 chr14 107349540 78490774 0.731170100961774 1.778556287658411 chr15 102531392 50073114 0.48836861592594005 1.6800812269536383 chr16 90354753 31614621 0.349894387957654 1.2189199872473395 chr17 81195210 39487089 0.48632288776640886 1.465931251209745 chr18 78077248 45671847 0.5849571824047897 1.5277129218094068 chr19 59128983 27307352 0.46182685063262463 1.536621979811813 chr20 63025520 49543030 0.786078877254801 1.9700686029347896 chr21 48129895 17987616 0.3737306304117223 1.1990003754399439 chr22 51304566 11036244 0.21511231573423698 0.8155986862339023 chrMT 16571 661 0.03988896264558566 0.2484194677413299 chrX 155270560 177214542 1.141327383632802 2.5814955067480962 chrY 59373566 1642629 0.027665998703867645 0.4237094158083073