BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068946.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 = 2,724,349 number of mapped reads = 2,292,552 (84.15%) number of supplementary alignments = 17,258 (0.63%) number of secondary alignments = 0 number of mapped bases = 153,892,314 bp number of sequenced bases = 153,823,919 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,311 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8867 >>>>>>> ACTG content number of A's = 43,178,498 bp (28.07%) number of C's = 26,975,973 bp (17.54%) number of T's = 50,989,408 bp (33.15%) number of G's = 32,297,187 bp (21%) number of N's = 382,853 bp (0.25%) GC percentage = 38.53% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 1,712,128 number of insertions = 14,115 mapped reads with insertion percentage = 0.61% number of deletions = 41,139 mapped reads with deletion percentage = 1.77% homopolymer indels = 48.31% >>>>>>> Coverage mean coverageData = 0.0497X std coverageData = 0.4582X There is a 4.02% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 14047063 0.056357183559434344 0.6665959364978739 chr2 243199373 8738394 0.03593098901616001 0.37212712388653596 chr3 198022430 16577938 0.08371747584351934 0.3465322720515947 chr4 191154276 5438501 0.028450846686788215 0.24794748415606113 chr5 180915260 3608006 0.019943071690027694 0.17648468801053555 chr6 171115067 12237405 0.07151564858984627 0.4381660116770829 chr7 159138663 11417026 0.07174262862821715 0.6964622993217461 chr8 146364022 5305906 0.03625143616236509 0.5797089668001215 chr9 141213431 14181653 0.10042708331334291 0.5684244063145638 chr10 135534747 7935098 0.05854659543504368 0.5704589985889592 chr11 135006516 5944504 0.04403123772188892 0.35996667733980836 chr12 133851895 10826346 0.08088302373305958 0.3449511015026302 chr13 115169878 588292 0.005108037016415004 0.1026595579461862 chr14 107349540 6016286 0.05604389175771037 0.32684632718938733 chr15 102531392 2082105 0.020307000220966473 0.16338310592354843 chr16 90354753 3623081 0.04009839969348375 0.29564746771357703 chr17 81195210 2165225 0.02666690559701736 0.22118652086165982 chr18 78077248 744758 0.009538732717628572 0.678544550834746 chr19 59128983 1588069 0.02685770868069894 0.39063966457333826 chr20 63025520 1708938 0.027115016266426678 0.2160686869184258 chr21 48129895 547777 0.011381221587954847 0.22169039215236655 chr22 51304566 244911 0.0047736686828225 0.0922587768198929 chrMT 16571 952755 57.49532315490918 26.920383132912985 chrX 155270560 16880414 0.10871612751316154 0.4576062820048935 chrY 59373566 491863 0.008284208497768182 0.1914709873800453