BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004151.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,300,187 number of mapped reads = 3,783,740 (87.99%) number of supplementary alignments = 26,571 (0.62%) number of secondary alignments = 0 number of mapped bases = 253,531,750 bp number of sequenced bases = 253,423,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 221,497 duplication rate = 4.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0739 >>>>>>> ACTG content number of A's = 70,596,185 bp (27.86%) number of C's = 45,958,640 bp (18.14%) number of T's = 82,067,197 bp (32.38%) number of G's = 54,773,907 bp (21.61%) number of N's = 27,767 bp (0.01%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 2,299,400 number of insertions = 20,698 mapped reads with insertion percentage = 0.54% number of deletions = 65,547 mapped reads with deletion percentage = 1.71% homopolymer indels = 47.71% >>>>>>> Coverage mean coverageData = 0.0819X std coverageData = 0.7581X There is a 6.26% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 25922802 0.10400295853224775 1.0812494086471691 chr2 243199373 16572871 0.06814520446975 0.7428296612509355 chr3 198022430 10758424 0.054329320168427384 0.2875323172845289 chr4 191154276 25573777 0.1337860577076497 0.4569827218805669 chr5 180915260 12258164 0.06775638495061169 0.31751668099695773 chr6 171115067 8959120 0.05235728306730582 0.3576688832686002 chr7 159138663 24536604 0.15418380133054152 2.2284743393598085 chr8 146364022 19409341 0.13261005494915956 1.0397510774932717 chr9 141213431 5708461 0.040424348870894584 0.4395388994911756 chr10 135534747 11929766 0.0880199820640828 0.5340934469336658 chr11 135006516 9209626 0.06821615928523035 0.4008524749464172 chr12 133851895 15715297 0.11740810244038756 0.42621525641103214 chr13 115169878 4489551 0.038981989717832295 0.24515548805148205 chr14 107349540 1812808 0.016886965701017442 0.21793076948733514 chr15 102531392 5996875 0.05848818476979226 0.30563245364299024 chr16 90354753 8290779 0.09175808382764325 0.3976285438459298 chr17 81195210 7277571 0.08963054593984054 0.39884084627945504 chr18 78077248 8408393 0.10769325527457116 0.816523221082718 chr19 59128983 1979003 0.033469254832270666 0.771055593975867 chr20 63025520 7363617 0.11683548188099042 0.4652764848457281 chr21 48129895 3985266 0.08280229990113214 0.3661463293189499 chr22 51304566 3030006 0.059059187831352083 0.2948705702776538 chrMT 16571 225053 13.581135719027216 8.387960799893586 chrX 155270560 13679174 0.08809895449594565 0.4150954735840953 chrY 59373566 439401 0.007400616631313673 0.1340507864920659