BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524446.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 = 3,918,833 number of mapped reads = 3,644,283 (92.99%) number of supplementary alignments = 8,851 (0.23%) number of secondary alignments = 0 number of mapped bases = 213,772,378 bp number of sequenced bases = 213,702,162 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 288,549 duplication rate = 5.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6497 >>>>>>> ACTG content number of A's = 53,475,568 bp (25.02%) number of C's = 39,848,444 bp (18.65%) number of T's = 68,478,610 bp (32.04%) number of G's = 51,895,064 bp (24.28%) number of N's = 4,476 bp (0%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 984,446 number of insertions = 16,385 mapped reads with insertion percentage = 0.45% number of deletions = 40,725 mapped reads with deletion percentage = 1.11% homopolymer indels = 41.24% >>>>>>> Coverage mean coverageData = 0.0691X std coverageData = 0.5788X There is a 5.41% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 20902879 0.08386289637368646 1.170706323223765 chr2 243199373 16693624 0.06864172301957373 0.6270469902758807 chr3 198022430 11842879 0.05980574523805207 0.30399835383935975 chr4 191154276 12202480 0.06383576792182248 0.3778228900575754 chr5 180915260 11544019 0.06380898438307527 0.31666967635071447 chr6 171115067 9230326 0.05394221655536622 0.41954718274900904 chr7 159138663 10749587 0.06754855669486176 0.8239232924678884 chr8 146364022 19821501 0.1354260475296313 0.6009589710139415 chr9 141213431 8967200 0.0635010419086836 0.4815187120082637 chr10 135534747 11185117 0.08252582638458018 0.5590304581995114 chr11 135006516 7333333 0.05431836341884417 0.552613193136798 chr12 133851895 9917863 0.07409579819546074 0.34097276487946243 chr13 115169878 4779477 0.041499366700727076 0.2561354870148506 chr14 107349540 5027172 0.046829935181836826 0.2833430786473193 chr15 102531392 5664284 0.05524438798217038 0.30862016116372964 chr16 90354753 6537245 0.07235087013076114 0.37384614867885363 chr17 81195210 7278707 0.08964453691295336 0.41057969425657376 chr18 78077248 5110052 0.06544866950228574 0.9453049679377311 chr19 59128983 4212634 0.07124482421759225 0.7903941371451058 chr20 63025520 6870942 0.10901841032013698 0.41925419950392273 chr21 48129895 2908540 0.06043104810430191 0.34559618227821287 chr22 51304566 1660045 0.03235667172391635 0.2213590471765104 chrMT 16571 72780 4.392010138193229 3.4682277321029265 chrX 155270560 12601983 0.08116144489979298 0.42613599049985956 chrY 59373566 657709 0.011077471748959799 0.28109202294490904