BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008817.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 = 2,049,763 number of mapped reads = 1,600,695 (78.09%) number of supplementary alignments = 11,406 (0.56%) number of secondary alignments = 0 number of mapped bases = 101,993,792 bp number of sequenced bases = 101,932,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,111 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1467 >>>>>>> ACTG content number of A's = 30,461,117 bp (29.88%) number of C's = 17,108,095 bp (16.78%) number of T's = 31,232,081 bp (30.64%) number of G's = 23,102,104 bp (22.66%) number of N's = 28,620 bp (0.03%) GC percentage = 39.45% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 1,090,149 number of insertions = 7,929 mapped reads with insertion percentage = 0.49% number of deletions = 40,026 mapped reads with deletion percentage = 2.47% homopolymer indels = 48.54% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.2563X There is a 2.79% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 7097364 0.028474809697665707 0.3226900004890983 chr2 243199373 9584361 0.03940948071440957 0.27556986953886276 chr3 198022430 8801500 0.04444698512183696 0.25068344316606067 chr4 191154276 5207752 0.02724371177550849 0.19619052854062669 chr5 180915260 3624907 0.020036491117443603 0.16861957514891276 chr6 171115067 4665619 0.027265974188000638 0.22301570974037613 chr7 159138663 5350980 0.033624638407324055 0.32786316224791934 chr8 146364022 9115723 0.06228117316972883 0.4009160601198173 chr9 141213431 3416866 0.024196466127928015 0.20899131576814156 chr10 135534747 6535357 0.048219051901133514 0.28769979709737686 chr11 135006516 6932854 0.05135199548442536 0.32586509232233896 chr12 133851895 5150824 0.03848151720227794 0.2309203549872516 chr13 115169878 2367135 0.02055342109505404 0.1724251134299757 chr14 107349540 3016295 0.02809788472312038 0.199501810072402 chr15 102531392 2720632 0.026534624634765518 0.1939148989075694 chr16 90354753 2481395 0.027462805415449477 0.2082232042633307 chr17 81195210 3472448 0.04276666074267189 0.27315517658355776 chr18 78077248 1446898 0.01853162140141005 0.28883389227407746 chr19 59128983 1480801 0.025043572963194715 0.2258754778546505 chr20 63025520 2195405 0.03483358804496972 0.2226379054683195 chr21 48129895 1298201 0.026972861669446818 0.19691004685000454 chr22 51304566 826521 0.016110086575919967 0.14793686785727414 chrMT 16571 30722 1.8539617403898376 2.880100833583343 chrX 155270560 4969509 0.03200548127088612 0.22375974498715379 chrY 59373566 203723 0.0034312070795949833 0.0798068153381764