BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013196.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 = 1,585,199 number of mapped reads = 1,308,711 (82.56%) number of supplementary alignments = 9,733 (0.61%) number of secondary alignments = 0 number of mapped bases = 83,892,886 bp number of sequenced bases = 83,848,572 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,589 duplication rate = 3.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6536 >>>>>>> ACTG content number of A's = 22,325,234 bp (26.63%) number of C's = 15,030,663 bp (17.93%) number of T's = 27,068,487 bp (32.28%) number of G's = 19,423,212 bp (23.16%) number of N's = 976 bp (0%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 644,287 number of insertions = 5,675 mapped reads with insertion percentage = 0.43% number of deletions = 25,749 mapped reads with deletion percentage = 1.95% homopolymer indels = 45.52% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.2742X There is a 2.3% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% 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 4600652 0.018457935958362166 0.32491157275313215 chr2 243199373 4886197 0.020091322357150977 0.3014981174486379 chr3 198022430 4147010 0.02094212256662036 0.1635425074122046 chr4 191154276 8529447 0.044620749158653404 0.2448164230422363 chr5 180915260 3620928 0.020014497395078778 0.16586852274458777 chr6 171115067 2213320 0.012934687978119426 0.1719301971364944 chr7 159138663 10310182 0.06478741121508605 0.66122391443851 chr8 146364022 5113852 0.03493926943330377 0.3505672504408032 chr9 141213431 2619336 0.018548773876898437 0.21823073058459472 chr10 135534747 4570147 0.03371937529790792 0.25887414023627825 chr11 135006516 4019560 0.02977308147111951 0.21947503825315082 chr12 133851895 2563304 0.019150300412257893 0.16264994009116962 chr13 115169878 2372444 0.02059951821777566 0.16212676580861066 chr14 107349540 1254741 0.011688368669302169 0.1339766765186118 chr15 102531392 2731788 0.026643430335950184 0.18855378954764052 chr16 90354753 2699069 0.02987190945007619 0.2029165161757532 chr17 81195210 3188023 0.03926368316554634 0.2435148638995558 chr18 78077248 2798920 0.03584808726864963 0.3186092017210734 chr19 59128983 2842507 0.048072989856767875 0.3156908697870422 chr20 63025520 2514799 0.03990128125876629 0.23229813717269504 chr21 48129895 1800261 0.03740421623608362 0.22699956699551382 chr22 51304566 628591 0.012252145354859838 0.12440093984895796 chrMT 16571 7901 0.47679681371069943 0.8519535194545133 chrX 155270560 3682975 0.02371972510435977 0.18823279599674814 chrY 59373566 176932 0.002979979339627335 0.07913157479257424