BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240027.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 = 1,308,775 number of mapped reads = 993,181 (75.89%) number of supplementary alignments = 6,571 (0.5%) number of secondary alignments = 0 number of mapped bases = 64,922,045 bp number of sequenced bases = 64,890,711 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,754 duplication rate = 10.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7253 >>>>>>> ACTG content number of A's = 17,884,272 bp (27.56%) number of C's = 11,539,343 bp (17.78%) number of T's = 21,320,866 bp (32.86%) number of G's = 14,140,433 bp (21.79%) number of N's = 5,797 bp (0.01%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 551,982 number of insertions = 4,752 mapped reads with insertion percentage = 0.47% number of deletions = 17,931 mapped reads with deletion percentage = 1.79% homopolymer indels = 49.28% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.2881X There is a 1.12% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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% 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 5148016 0.0206539746193852 0.3936858669645385 chr2 243199373 7010428 0.02882584734295347 0.33843093232133303 chr3 198022430 4040726 0.020405395489793757 0.24523103074383396 chr4 191154276 4198956 0.021966320021007534 0.25391979106677093 chr5 180915260 3436699 0.0189961808639028 0.23502507703891776 chr6 171115067 3308436 0.01933456859178859 0.24908562930933817 chr7 159138663 3848496 0.02418328725056588 0.3655513994698714 chr8 146364022 3662196 0.025021148981544113 0.397552313532486 chr9 141213431 2431795 0.01722070615223562 0.2529526081339409 chr10 135534747 3123445 0.023045344969729424 0.2960183934979438 chr11 135006516 2775707 0.020559800239567695 0.2609324621764493 chr12 133851895 3289848 0.024578269885532814 0.26830246872702557 chr13 115169878 1737292 0.015084603979523187 0.2071757208887047 chr14 107349540 2123204 0.019778417308541796 0.24249365053731484 chr15 102531392 1825885 0.017808058238397855 0.22535778679897664 chr16 90354753 1953159 0.021616560669475794 0.24946124136637188 chr17 81195210 1489028 0.018338865063591805 0.22820309504530562 chr18 78077248 1619025 0.02073619449292065 0.3568746107463524 chr19 59128983 1134194 0.019181693011699526 0.2939287823624224 chr20 63025520 1337668 0.021224227900063338 0.2502496046645482 chr21 48129895 1050523 0.02182682925030275 0.25391856428156917 chr22 51304566 534987 0.010427668367762823 0.1633187681035724 chrMT 16571 10318 0.6226540341560558 1.2584623048076231 chrX 155270560 3652505 0.023523487002301016 0.26906548811952136 chrY 59373566 179509 0.0030233824931451816 0.08557672744974372