BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038450.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 16,570,926 number of mapped reads = 15,964,619 (96.34%) number of supplementary alignments = 166,592 (1.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,032,664 number of mapped paired reads (second in pair) = 7,931,955 number of mapped paired reads (both in pair) = 15,844,582 number of mapped paired reads (singletons) = 120,037 number of mapped bases = 2,351,390,167 bp number of sequenced bases = 2,350,571,807 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,555,233 duplication rate = 7.51% >>>>>>> Insert size mean insert size = 105,929.3981 std insert size = 3,250,603.06 median insert size = 288 >>>>>>> Mapping quality mean mapping quality = 54.3373 >>>>>>> ACTG content number of A's = 674,290,539 bp (28.69%) number of C's = 503,224,764 bp (21.41%) number of T's = 669,174,683 bp (28.47%) number of G's = 503,660,362 bp (21.43%) number of N's = 221,459 bp (0.01%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 20,520,459 number of insertions = 276,978 mapped reads with insertion percentage = 1.64% number of deletions = 297,746 mapped reads with deletion percentage = 1.78% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 0.7596X std coverageData = 7.0065X There is a 43.68% of reference with a coverageData >= 1X There is a 18.72% of reference with a coverageData >= 2X There is a 6.84% of reference with a coverageData >= 3X There is a 2.6% of reference with a coverageData >= 4X There is a 0.94% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% 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 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 0.01% 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 200698130 0.8052061382828009 17.082891129366143 chr2 243199373 199670095 0.8210140204596662 5.971759172694674 chr3 198022430 155255460 0.7840296677502645 1.163894619477575 chr4 191154276 131305896 0.6869105873415042 5.084035858269534 chr5 180915260 147002723 0.8125501574604597 1.1411650734332632 chr6 171115067 133633201 0.7809551978260336 3.1482036123721526 chr7 159138663 122793647 0.7716141677022886 5.545526800346995 chr8 146364022 127383677 0.8703209658996662 4.254536230133766 chr9 141213431 100068988 0.7086364752372598 7.830719562489932 chr10 135534747 119790035 0.8838326528915865 15.57374175823972 chr11 135006516 108647575 0.8047580088652906 2.9565648589011375 chr12 133851895 102419305 0.7651688831151774 1.276920780928183 chr13 115169878 75193325 0.6528905500794226 1.0248008761648677 chr14 107349540 73341849 0.6832059923125893 1.0966638549265917 chr15 102531392 67472050 0.6580623620129921 1.0416330836133794 chr16 90354753 74221040 0.8214403507915073 4.287071214389917 chr17 81195210 68595137 0.8448175329554539 3.860222674101498 chr18 78077248 72878160 0.933410972681824 6.584161561520212 chr19 59128983 48641335 0.8226310099059204 7.013746851446834 chr20 63025520 57582324 0.9136350481519232 2.007983327946036 chr21 48129895 30273684 0.6289995853928209 2.8151945972302665 chr22 51304566 25864397 0.5041344078419843 0.9355681887423757 chrMT 16571 3539546 213.59881721078995 28.251829725337103 chrX 155270560 99326407 0.6396989036427768 1.6028608958745811 chrY 59373566 5792181 0.09755487820960594 5.078934385280464