BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549096.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 = 7,586,928 number of mapped reads = 6,662,102 (87.81%) number of secondary alignments = 0 number of mapped bases = 264,654,168 bp number of sequenced bases = 264,629,967 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,320 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2524 >>>>>>> ACTG content number of A's = 78,392,371 bp (29.62%) number of C's = 54,050,829 bp (20.43%) number of T's = 79,468,534 bp (30.03%) number of G's = 52,654,173 bp (19.9%) number of N's = 64,060 bp (0.02%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 1,037,969 number of insertions = 5,807 mapped reads with insertion percentage = 0.09% number of deletions = 19,239 mapped reads with deletion percentage = 0.29% homopolymer indels = 45.78% >>>>>>> Coverage mean coverageData = 0.0855X std coverageData = 0.645X There is a 7.29% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 21480428 0.08618003804291424 1.5716128602131771 chr2 243199373 23196648 0.09538119985202428 0.495828072343367 chr3 198022430 18832143 0.09510106001628199 0.3495459238088318 chr4 191154276 18506348 0.09681367525359465 0.36079055540893695 chr5 180915260 17384349 0.0960911147019881 0.35755843511035357 chr6 171115067 16143645 0.09434379615443216 0.44016048711853506 chr7 159138663 14757139 0.09273132450534663 0.6729234735060663 chr8 146364022 14182477 0.09689865587323092 0.6633022445743662 chr9 141213431 11171060 0.07910763105812506 0.47716248057319766 chr10 135534747 12755098 0.09410943158362188 0.5639521841904425 chr11 135006516 12316427 0.0912283893023356 0.4963980703634911 chr12 133851895 12160443 0.0908499875926299 0.3557388323264989 chr13 115169878 9167040 0.07959581237031439 0.312265562068047 chr14 107349540 8287008 0.07719649287737981 0.36205116693358746 chr15 102531392 7432771 0.07249263718179111 0.30021463645570357 chr16 90354753 7024877 0.0777477306589505 0.38225052598046094 chr17 81195210 6154507 0.07579889257014052 0.3660617952848957 chr18 78077248 7267418 0.09307984318299743 0.9227678595890932 chr19 59128983 4180868 0.07070759190970695 1.1518880607817157 chr20 63025520 5351330 0.08490735181558201 0.3405157675187391 chr21 48129895 3480352 0.07231164746983137 0.3480912265264745 chr22 51304566 2491929 0.04857129090615443 0.28327524154894074 chrMT 16571 14291 0.8624102347474504 1.4622958183145411 chrX 155270560 8748059 0.05634074482632123 0.33261978850941043 chrY 59373566 2167513 0.03650636379159035 0.33065904680185443