BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716611.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 = 798,444 number of mapped reads = 660,664 (82.74%) number of supplementary alignments = 18,759 (2.35%) number of secondary alignments = 0 number of mapped bases = 50,599,433 bp number of sequenced bases = 50,580,304 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,310 duplication rate = 1.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2556 >>>>>>> ACTG content number of A's = 13,224,075 bp (26.14%) number of C's = 10,075,385 bp (19.92%) number of T's = 14,991,654 bp (29.64%) number of G's = 12,282,542 bp (24.28%) number of N's = 6,648 bp (0.01%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 370,456 number of insertions = 4,253 mapped reads with insertion percentage = 0.64% number of deletions = 10,696 mapped reads with deletion percentage = 1.6% homopolymer indels = 40.85% >>>>>>> Coverage mean coverageData = 0.0163X std coverageData = 0.1685X There is a 1.53% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5111598 0.020507864652421468 0.24275268148250206 chr2 243199373 4095424 0.01683978025716374 0.2178434824618454 chr3 198022430 3630193 0.018332231353791587 0.14381661047210037 chr4 191154276 2057437 0.010763227708283125 0.11194098382382674 chr5 180915260 3429161 0.018954514948048052 0.14395795799069508 chr6 171115067 3357439 0.019620943139974926 0.15583655858947326 chr7 159138663 2751365 0.017289104659626305 0.21266030560100974 chr8 146364022 3431352 0.0234439581060433 0.20074721055708564 chr9 141213431 2354937 0.016676437809941748 0.1600472248078897 chr10 135534747 2644385 0.019510753209285882 0.20485865401668854 chr11 135006516 1944907 0.01440602318779932 0.14766091143718177 chr12 133851895 2166010 0.016182139221861597 0.13357105630825458 chr13 115169878 1529271 0.013278393852253625 0.11988752144181557 chr14 107349540 1215846 0.011326047601135505 0.1179520549011577 chr15 102531392 1040444 0.010147565342719623 0.10495753649668454 chr16 90354753 1255233 0.01389227415629148 0.12824058038734631 chr17 81195210 1635513 0.020142973951295894 0.15943943298786167 chr18 78077248 1243581 0.015927572139837715 0.21512454747000276 chr19 59128983 1014927 0.017164628047128767 0.20093240001684898 chr20 63025520 837536 0.013288839187681435 0.12196134514684757 chr21 48129895 869107 0.01805752952504883 0.14230511162007198 chr22 51304566 708323 0.013806237051103794 0.12430820912166315 chrMT 16571 3836 0.23148874539858788 0.5182642756072858 chrX 155270560 2150247 0.013848388258534006 0.13044632682703192 chrY 59373566 121361 0.0020440241032516054 0.07720679120304837