BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708605.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 5,648,554 number of mapped reads = 5,464,795 (96.75%) number of supplementary alignments = 158 (0%) number of secondary alignments = 0 number of mapped bases = 272,593,046 bp number of sequenced bases = 272,569,231 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,287 duplication rate = 1.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7625 >>>>>>> ACTG content number of A's = 84,338,546 bp (30.94%) number of C's = 51,757,326 bp (18.99%) number of T's = 83,972,129 bp (30.81%) number of G's = 52,490,298 bp (19.26%) number of N's = 10,932 bp (0%) GC percentage = 38.25% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 392,418 number of insertions = 17,041 mapped reads with insertion percentage = 0.31% number of deletions = 13,881 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.64% >>>>>>> Coverage mean coverageData = 0.0881X std coverageData = 0.3107X There is a 8.07% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% 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 23345673 0.09366344968905815 0.3235743357736038 chr2 243199373 22198828 0.09127831098479025 0.3142150593074188 chr3 198022430 20105599 0.10153192746902459 0.33173408138138905 chr4 191154276 20953313 0.10961467061296604 0.34414709529434895 chr5 180915260 20190662 0.11160286865795621 0.3476043349683464 chr6 171115067 16629191 0.0971813370473098 0.3248695899143892 chr7 159138663 14784690 0.09290445025292188 0.3185410991932203 chr8 146364022 15555615 0.10628031935334491 0.3401268070196428 chr9 141213431 10877319 0.07702751022316001 0.2907311098335918 chr10 135534747 10915301 0.08053507489116425 0.29468197213967545 chr11 135006516 13174465 0.09758391957911128 0.3287480351508885 chr12 133851895 12344795 0.09222727104461241 0.31738027969475063 chr13 115169878 10805829 0.09382513194986626 0.32118060194446557 chr14 107349540 9356019 0.08715471906074307 0.31116991556602724 chr15 102531392 7489715 0.07304801830838306 0.2842778633097256 chr16 90354753 5359854 0.059320111250815995 0.25458705469135473 chr17 81195210 4681738 0.057660273309226 0.251452678993845 chr18 78077248 7581447 0.09710187275043301 0.3236473620395067 chr19 59128983 2171081 0.03671771253024934 0.19825753692610523 chr20 63025520 4137148 0.06564242548097977 0.26743839399706004 chr21 48129895 3262034 0.06777563092543626 0.2747202159713184 chr22 51304566 1682882 0.03280179779710055 0.18884579086031683 chrMT 16571 545 0.03288878160642086 0.18302133351713004 chrX 155270560 14643008 0.09430640296524982 0.31935448642543 chrY 59373566 346295 0.00583247770565103 0.08093976290358103