BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714119.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 = 614,468 number of mapped reads = 513,215 (83.52%) number of supplementary alignments = 16,669 (2.71%) number of secondary alignments = 0 number of mapped bases = 64,959,310 bp number of sequenced bases = 63,787,647 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 500,263 duplication rate = 34.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 27.147 >>>>>>> ACTG content number of A's = 18,005,943 bp (28.23%) number of C's = 13,141,673 bp (20.6%) number of T's = 17,350,028 bp (27.2%) number of G's = 15,289,535 bp (23.97%) number of N's = 468 bp (0%) GC percentage = 44.57% >>>>>>> Mismatches and indels general error rate = 0.0433 number of mismatches = 2,513,049 number of insertions = 87,033 mapped reads with insertion percentage = 16.61% number of deletions = 162,960 mapped reads with deletion percentage = 30.53% homopolymer indels = 25.4% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 20.6572X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 1939423 0.007781015719114296 4.6304541360096465 chr2 243199373 3942408 0.01621060100348203 7.931053503181381 chr3 198022430 815521 0.004118326393631267 1.740026667447104 chr4 191154276 5058568 0.02646327409385286 17.971556904022602 chr5 180915260 1666442 0.009211174336537448 4.635212062211806 chr6 171115067 16211778 0.09474196681932165 66.31960071001035 chr7 159138663 887838 0.005579021359504573 2.316480947180547 chr8 146364022 8593984 0.058716506164335935 44.42453048272825 chr9 141213431 1315686 0.009317003281366346 5.921358489142007 chr10 135534747 3062955 0.02259903875424654 14.853839109108188 chr11 135006516 2981858 0.022086770982224294 12.667956778441116 chr12 133851895 1460047 0.010907929245230335 4.6355604619837 chr13 115169878 245390 0.002130678648457021 0.639101325872583 chr14 107349540 1245490 0.011602192240413886 3.9956247586081455 chr15 102531392 696148 0.006789608396226591 3.0758661040415 chr16 90354753 753218 0.008336229971211365 2.7966845339958324 chr17 81195210 441464 0.005437069502006338 1.6252441232936667 chr18 78077248 107047 0.0013710396145110032 0.39110097323970666 chr19 59128983 112394 0.0019008275518623413 0.6002361505355781 chr20 63025520 612623 0.009720237135687258 2.9218791626211273 chr21 48129895 2487226 0.051677361855869415 25.33051594506096 chr22 51304566 1202579 0.023439999472951393 12.851576997137514 chrMT 16571 191190 11.537625973085511 97.335725644141 chrX 155270560 8756775 0.056396879099296096 23.89127955754682 chrY 59373566 171258 0.002884414926332705 0.8093658516400909