BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080656.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,460,392 number of mapped reads = 1,311,114 (89.78%) number of supplementary alignments = 9,570 (0.66%) number of secondary alignments = 0 number of mapped bases = 84,684,429 bp number of sequenced bases = 84,646,858 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,475 duplication rate = 2.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5821 >>>>>>> ACTG content number of A's = 22,287,334 bp (26.33%) number of C's = 15,500,419 bp (18.31%) number of T's = 26,718,119 bp (31.56%) number of G's = 20,137,569 bp (23.79%) number of N's = 3,417 bp (0%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 633,174 number of insertions = 6,894 mapped reads with insertion percentage = 0.52% number of deletions = 23,231 mapped reads with deletion percentage = 1.75% homopolymer indels = 45.04% >>>>>>> Coverage mean coverageData = 0.0274X std coverageData = 0.2667X There is a 2.44% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 8640256 0.03466493269037833 0.3351776097213989 chr2 243199373 6268612 0.025775609215900403 0.48613003484406075 chr3 198022430 5376616 0.027151550458198094 0.18043599415853803 chr4 191154276 4378367 0.02290488652213043 0.17498982555511727 chr5 180915260 4458180 0.024642365713096838 0.17195358642760955 chr6 171115067 4902003 0.028647407185949325 0.23257161913786392 chr7 159138663 5158214 0.0324133300026531 0.45205366755450227 chr8 146364022 7405675 0.05059764618930737 0.2945239079331215 chr9 141213431 3103692 0.021978730904144664 0.2141655926793964 chr10 135534747 3976551 0.029339716109847463 0.21594875429670973 chr11 135006516 3748056 0.027762037796753455 0.23785548344156987 chr12 133851895 3220614 0.024061026554760393 0.1720166212351106 chr13 115169878 2153709 0.01870028029377612 0.14992597119863038 chr14 107349540 2124773 0.019793033114068305 0.17232358774996753 chr15 102531392 1910271 0.01863108422442953 0.15746010508039618 chr16 90354753 2286574 0.025306626647521244 0.18392180399265892 chr17 81195210 1788863 0.02203163216155239 0.17736217380844457 chr18 78077248 2445149 0.031317048982054285 0.3154568024213348 chr19 59128983 1636882 0.02768324291997378 0.24397848410853376 chr20 63025520 1918851 0.030445619488740434 0.1960915444540034 chr21 48129895 1207744 0.025093426860789952 0.17914922343406522 chr22 51304566 910571 0.017748342321032402 0.14565352830772652 chrMT 16571 9843 0.5939894997284413 0.8564363101189898 chrX 155270560 5444880 0.03506704683746874 0.21857957270055697 chrY 59373566 209483 0.0035282199489247456 0.07980841462428381