BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716891.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,345,528 number of mapped reads = 1,991,650 (84.91%) number of supplementary alignments = 45,129 (1.92%) number of secondary alignments = 0 number of mapped bases = 148,386,266 bp number of sequenced bases = 148,334,762 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,299 duplication rate = 2.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9271 >>>>>>> ACTG content number of A's = 39,007,244 bp (26.3%) number of C's = 30,320,782 bp (20.44%) number of T's = 43,375,146 bp (29.24%) number of G's = 35,613,698 bp (24.01%) number of N's = 17,892 bp (0.01%) GC percentage = 44.45% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,089,721 number of insertions = 12,115 mapped reads with insertion percentage = 0.6% number of deletions = 29,996 mapped reads with deletion percentage = 1.49% homopolymer indels = 39.97% >>>>>>> Coverage mean coverageData = 0.0479X std coverageData = 0.3671X There is a 4.07% of reference with a coverageData >= 1X There is a 0.52% 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 11823083 0.04743451772583548 0.39741464255292847 chr2 243199373 12749328 0.052423358838182534 0.5462393011797052 chr3 198022430 9858470 0.04978461278351144 0.25398076181932716 chr4 191154276 9432009 0.04934239085501807 0.2799115647176417 chr5 180915260 8907907 0.04923800789386147 0.255243898591693 chr6 171115067 8508486 0.04972376862640623 0.2915668586323426 chr7 159138663 8155320 0.05124662885976364 0.47227380387104906 chr8 146364022 7536043 0.05148835688595658 0.4630938229690239 chr9 141213431 6260942 0.04433673168099712 0.39266226542609406 chr10 135534747 7050186 0.05201755384543567 0.3570662925636742 chr11 135006516 6819008 0.05050873248221589 0.401710404417743 chr12 133851895 6791857 0.050741582702284495 0.2623671475438874 chr13 115169878 4677668 0.04061537687831883 0.228547490920892 chr14 107349540 4457978 0.04152768609907411 0.27571640122491003 chr15 102531392 4312574 0.042061010934095186 0.23647703117252267 chr16 90354753 4437275 0.04910948071541959 0.28309686295532854 chr17 81195210 4098548 0.05047770675142044 0.28013648244757855 chr18 78077248 4124379 0.0528243387881704 0.7508483656763052 chr19 59128983 3014892 0.050988395995243144 0.3774309852078117 chr20 63025520 3156996 0.05009075688705147 0.26732849674661857 chr21 48129895 1977688 0.04109063607971719 0.26129251317530083 chr22 51304566 1711820 0.033365841161194114 0.2088391528974072 chrMT 16571 19435 1.1728320560014482 1.5863635243279133 chrX 155270560 8134387 0.05238846952055818 0.3240925009587678 chrY 59373566 369987 0.006231510500817822 0.17102409692176238