BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714089.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 528,416 number of mapped reads = 311,288 (58.91%) number of supplementary alignments = 11,722 (2.22%) number of secondary alignments = 0 number of mapped bases = 40,267,597 bp number of sequenced bases = 39,441,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 274,183 duplication rate = 43.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.0181 >>>>>>> ACTG content number of A's = 10,448,319 bp (26.49%) number of C's = 7,826,339 bp (19.84%) number of T's = 9,889,000 bp (25.07%) number of G's = 11,277,021 bp (28.59%) number of N's = 384 bp (0%) GC percentage = 48.44% >>>>>>> Mismatches and indels general error rate = 0.0441 number of mismatches = 1,600,238 number of insertions = 48,449 mapped reads with insertion percentage = 14.78% number of deletions = 138,039 mapped reads with deletion percentage = 41.14% homopolymer indels = 31.06% >>>>>>> Coverage mean coverageData = 0.013X std coverageData = 4.7839X There is a 0.04% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 2774506 0.011131390521189513 2.5610172129444932 chr2 243199373 6282230 0.025831604426052528 14.295520071977315 chr3 198022430 2396525 0.012102290634449845 4.556617566124697 chr4 191154276 1236090 0.0064664522597443755 1.476597484753247 chr5 180915260 1677699 0.009273396837834465 1.376291377585382 chr6 171115067 1473362 0.008610358081442355 1.4264302421877326 chr7 159138663 1621593 0.010189811636157833 1.8730377859368799 chr8 146364022 2704278 0.018476384859115173 5.396004900479788 chr9 141213431 1253762 0.008878489752153957 2.3785565872695895 chr10 135534747 1916373 0.01413934833995005 2.728027714596225 chr11 135006516 1601944 0.011865679135072266 2.010327875629065 chr12 133851895 1777263 0.013277832189077339 2.968398759070376 chr13 115169878 1127755 0.009792100326788572 2.34374414346652 chr14 107349540 1240541 0.011556090505837287 2.112973145625592 chr15 102531392 1332615 0.012997141402313157 2.1991570184957108 chr16 90354753 770101 0.008523082344102031 1.4709409231379125 chr17 81195210 1173883 0.014457540044542036 3.2422011836075306 chr18 78077248 933938 0.011961717708083153 2.0769800307715176 chr19 59128983 1060910 0.017942300817181314 3.313788725544874 chr20 63025520 824299 0.013078813153782785 1.7722737298812976 chr21 48129895 441162 0.009166070277111554 2.3622759520170757 chr22 51304566 255479 0.004979654247538124 0.70201564043751 chrMT 16571 85093 5.135055216945266 35.880549438678415 chrX 155270560 3998632 0.025752673269163195 3.2582834226849258 chrY 59373566 307564 0.005180150371968562 1.5104813979899339