BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472787.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,790,200 number of mapped reads = 14,672,303 (99.2%) number of supplementary alignments = 52,022 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,356,956 number of mapped paired reads (second in pair) = 7,315,347 number of mapped paired reads (both in pair) = 14,602,536 number of mapped paired reads (singletons) = 69,767 number of mapped bases = 1,444,184,028 bp number of sequenced bases = 1,443,998,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,923,666 duplication rate = 46.48% >>>>>>> Insert size mean insert size = 24,579.9807 std insert size = 1,512,815.8492 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 55.3111 >>>>>>> ACTG content number of A's = 392,174,092 bp (27.16%) number of C's = 331,778,916 bp (22.98%) number of T's = 390,085,969 bp (27.01%) number of G's = 329,678,565 bp (22.83%) number of N's = 281,086 bp (0.02%) GC percentage = 45.81% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 8,363,634 number of insertions = 82,269 mapped reads with insertion percentage = 0.55% number of deletions = 75,911 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.4665X std coverageData = 15.5521X There is a 4.39% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 148135621 0.594323979638149 18.887794667860817 chr2 243199373 129507329 0.5325150612127606 17.239852875884367 chr3 198022430 152433135 0.7697771156530097 18.046487848984412 chr4 191154276 51651623 0.2702090901696596 10.903756640264271 chr5 180915260 75040612 0.4147832084479772 12.468736975741347 chr6 171115067 78827469 0.46066936349912424 11.885370370857308 chr7 159138663 69310985 0.43553831415562416 16.259899942031073 chr8 146364022 73541086 0.5024533009895014 16.19971776825512 chr9 141213431 84752369 0.600172153596353 18.962730013763803 chr10 135534747 33483126 0.2470445899751449 7.875800716235037 chr11 135006516 63445739 0.4699457543219618 13.240207481580821 chr12 133851895 59619460 0.44541364169704134 11.775590913113463 chr13 115169878 37144110 0.3225158404700229 17.074078047776386 chr14 107349540 40138295 0.3739028131839224 12.180851131804642 chr15 102531392 46064841 0.449275486282289 21.501416208800947 chr16 90354753 57870275 0.6404784815249287 19.097468319829783 chr17 81195210 57693212 0.710549452363015 18.331131405191798 chr18 78077248 32308828 0.4138059271761218 25.107455450725027 chr19 59128983 24897748 0.42107519420721307 10.131272951526393 chr20 63025520 29064184 0.46114945184109546 13.41902300362199 chr21 48129895 4456100 0.09258486851051721 3.1374309476611986 chr22 51304566 19110300 0.3724873142869974 9.690462324035506 chrMT 16571 773 0.04664775813167582 0.22714008586919796 chrX 155270560 73605542 0.4740469925528703 15.41487770069604 chrY 59373566 2081266 0.03505374765598549 1.2816495040690845