BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068944.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 = 1,290,863 number of mapped reads = 761,550 (59%) number of supplementary alignments = 4,427 (0.34%) number of secondary alignments = 0 number of mapped bases = 48,573,272 bp number of sequenced bases = 48,547,278 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,178 duplication rate = 6.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3904 >>>>>>> ACTG content number of A's = 12,973,852 bp (26.72%) number of C's = 8,217,596 bp (16.93%) number of T's = 16,335,182 bp (33.65%) number of G's = 10,912,560 bp (22.48%) number of N's = 108,088 bp (0.22%) GC percentage = 39.41% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 542,621 number of insertions = 4,190 mapped reads with insertion percentage = 0.55% number of deletions = 16,639 mapped reads with deletion percentage = 2.16% homopolymer indels = 48.88% >>>>>>> Coverage mean coverageData = 0.0157X std coverageData = 0.1901X There is a 1.14% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.09% 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% 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 5311587 0.021310225742627135 0.267961469068093 chr2 243199373 3951979 0.01624995554573243 0.19089742309464708 chr3 198022430 4842213 0.02445285112398631 0.21196857350862083 chr4 191154276 3550974 0.018576482170872287 0.18632303871434247 chr5 180915260 3141448 0.01736419581189558 0.1783500720575295 chr6 171115067 2565931 0.014995353974293801 0.1757275207660266 chr7 159138663 2072040 0.013020343145650282 0.18847622346697432 chr8 146364022 2862441 0.019556998782118737 0.2592265620888489 chr9 141213431 1752519 0.012410427163971394 0.16514161576816228 chr10 135534747 2177236 0.01606404297194726 0.18430370719720973 chr11 135006516 1987819 0.014723874512842032 0.17133416074147229 chr12 133851895 2151818 0.016076111585868844 0.1716453298723611 chr13 115169878 1190729 0.01033889260523485 0.13621741684074914 chr14 107349540 1198947 0.01116862727124867 0.14250734238149834 chr15 102531392 979302 0.0095512406580806 0.1293790703232101 chr16 90354753 996835 0.011032457805512456 0.14132103263628068 chr17 81195210 1034686 0.01274319014631528 0.15432457865008675 chr18 78077248 905199 0.01159363352560787 0.24010425592502507 chr19 59128983 663708 0.01122474912176318 0.1798833930812707 chr20 63025520 894320 0.014189807557319639 0.1626800437952561 chr21 48129895 586754 0.012191050905055996 0.15025386501644106 chr22 51304566 600187 0.01169851042108026 0.14325772669710088 chrMT 16571 97263 5.869470762174884 4.22778583560699 chrX 155270560 2873184 0.018504370693323963 0.1882950386423957 chrY 59373566 184153 0.0031015991190423025 0.06992193273410634