BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548960.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,551,623 number of mapped reads = 9,148,440 (86.7%) number of secondary alignments = 0 number of mapped bases = 361,350,254 bp number of sequenced bases = 361,317,174 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 518,398 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.0011 >>>>>>> ACTG content number of A's = 100,121,578 bp (27.71%) number of C's = 79,353,699 bp (21.96%) number of T's = 102,192,326 bp (28.28%) number of G's = 79,649,052 bp (22.04%) number of N's = 519 bp (0%) GC percentage = 44.01% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,188,778 number of insertions = 12,746 mapped reads with insertion percentage = 0.14% number of deletions = 25,991 mapped reads with deletion percentage = 0.28% homopolymer indels = 37.5% >>>>>>> Coverage mean coverageData = 0.1167X std coverageData = 1.1737X There is a 9.09% of reference with a coverageData >= 1X There is a 1.7% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 29205545 0.1171734091687579 2.0316526243014095 chr2 243199373 30733788 0.1263728093575307 1.2665806517038443 chr3 198022430 24450772 0.12347475990472392 0.43599650279590524 chr4 191154276 23544441 0.12316983691225405 0.527943534503394 chr5 180915260 21894701 0.12102185852094512 0.4652406823585663 chr6 171115067 20781377 0.12144679813613374 0.4865513374245666 chr7 159138663 21037211 0.13219421731600195 1.975502511706105 chr8 146364022 18814403 0.12854527187015946 1.9511520579484756 chr9 141213431 15391468 0.1089943632911235 1.304611412785471 chr10 135534747 17286093 0.12753993630873123 0.9526874839428593 chr11 135006516 16813909 0.12454146287279941 0.7952355116504468 chr12 133851895 16707038 0.12481734382617445 0.5060390016462916 chr13 115169878 11269943 0.09785495301123788 0.37259473408514554 chr14 107349540 10998973 0.10245943298872077 0.7140241155676301 chr15 102531392 10380894 0.10124600668642049 0.40248804400918553 chr16 90354753 10483325 0.11602405686394826 0.6067102996388231 chr17 81195210 10103564 0.12443546854549671 0.49334954665739406 chr18 78077248 9640384 0.12347238468241094 2.4382166649880865 chr19 59128983 8333917 0.14094470388574076 2.1218894247017612 chr20 63025520 7360359 0.11678378853518384 0.5042330332742179 chr21 48129895 4636004 0.09632275324930586 0.638179470994846 chr22 51304566 4284949 0.08351983720123468 0.5640512409357652 chrMT 16571 10712 0.6464305111339086 1.0462549736277964 chrX 155270560 13798221 0.08886566133335257 0.6868596929478623 chrY 59373566 3388263 0.05706686036004642 0.5327933139683849