BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716136.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 = 1,925,821 number of mapped reads = 1,774,429 (92.14%) number of supplementary alignments = 10,316 (0.54%) number of secondary alignments = 0 number of mapped bases = 103,282,166 bp number of sequenced bases = 103,251,505 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,367 duplication rate = 2.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2241 >>>>>>> ACTG content number of A's = 27,092,202 bp (26.24%) number of C's = 21,514,679 bp (20.84%) number of T's = 30,955,607 bp (29.98%) number of G's = 23,687,684 bp (22.94%) number of N's = 1,333 bp (0%) GC percentage = 43.78% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 516,543 number of insertions = 7,726 mapped reads with insertion percentage = 0.43% number of deletions = 19,385 mapped reads with deletion percentage = 1.08% homopolymer indels = 40.77% >>>>>>> Coverage mean coverageData = 0.0334X std coverageData = 0.3221X There is a 2.96% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9475388 0.03801550408173306 0.4617601746369267 chr2 243199373 10131574 0.041659539969290955 0.3964730669583203 chr3 198022430 7751717 0.03914565132848839 0.23238833272822634 chr4 191154276 5658716 0.029602874277319332 0.2053237585557731 chr5 180915260 5237820 0.028951786598875075 0.18750455673033664 chr6 171115067 5717036 0.033410476939473716 0.21836934506882924 chr7 159138663 5877196 0.036931289287003746 0.7278339933327689 chr8 146364022 7206333 0.04923568580262163 0.3358178479993377 chr9 141213431 4311049 0.030528604605605823 0.22678399191884857 chr10 135534747 4868627 0.03592161499368129 0.4033654076418956 chr11 135006516 3051684 0.022603975648108718 0.20882170766749805 chr12 133851895 4856597 0.03628336378801361 0.23184001079407512 chr13 115169878 2643142 0.022949941824198163 0.16607965931993074 chr14 107349540 3358848 0.031288890478710946 0.19804829003880722 chr15 102531392 2457368 0.02396698174155287 0.17650967605580264 chr16 90354753 3185862 0.035259484357175984 0.21607184930685353 chr17 81195210 4416311 0.05439127505181648 0.2685532746412755 chr18 78077248 2371402 0.03037251005568229 0.34779532209280684 chr19 59128983 2147068 0.036311600353417205 0.4139453665049592 chr20 63025520 2340016 0.037128071295564086 0.2210721446981764 chr21 48129895 785352 0.01631734289052573 0.15125053084573764 chr22 51304566 1581689 0.030829400252601297 0.19308989512633637 chrMT 16571 59581 3.5954981594351576 2.887174010744851 chrX 155270560 3562519 0.022943943784320738 0.19196912220620121 chrY 59373566 229271 0.0038614995771013654 0.101060853061516