BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013179.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 = 2,385,631 number of mapped reads = 2,136,822 (89.57%) number of supplementary alignments = 14,035 (0.59%) number of secondary alignments = 0 number of mapped bases = 139,735,349 bp number of sequenced bases = 139,657,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,979 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1554 >>>>>>> ACTG content number of A's = 38,073,480 bp (27.26%) number of C's = 26,602,984 bp (19.05%) number of T's = 43,107,933 bp (30.87%) number of G's = 31,840,636 bp (22.8%) number of N's = 32,941 bp (0.02%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,184,172 number of insertions = 9,479 mapped reads with insertion percentage = 0.44% number of deletions = 44,284 mapped reads with deletion percentage = 2.04% homopolymer indels = 43.81% >>>>>>> Coverage mean coverageData = 0.0451X std coverageData = 0.389X There is a 3.85% of reference with a coverageData >= 1X There is a 0.48% 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 9918531 0.03979340536928893 0.6592745525223593 chr2 243199373 15481029 0.06365571098737989 0.46783743514675824 chr3 198022430 8584609 0.04335170010791202 0.23557741743689883 chr4 191154276 8326608 0.043559621967337 0.24654672313668943 chr5 180915260 8113465 0.044846769697592125 0.24007734634289785 chr6 171115067 6789528 0.039678142427983856 0.2883544134945127 chr7 159138663 8807207 0.05534297469873804 0.6909875370067554 chr8 146364022 8410440 0.05746248213922408 0.3893573782042022 chr9 141213431 4700081 0.03328352669230167 0.3072160084369739 chr10 135534747 6273516 0.04628714140736176 0.4183528878940307 chr11 135006516 5540786 0.041040878352864095 0.29614577456300956 chr12 133851895 7117546 0.053174786953894077 0.2636382981489817 chr13 115169878 3415019 0.02965201543410509 0.19620514422735677 chr14 107349540 4895740 0.04560559830996947 0.2626806374896464 chr15 102531392 4006092 0.039071858109563165 0.2233840947429381 chr16 90354753 5048771 0.055877204379054635 0.30026199202306947 chr17 81195210 3572519 0.04399913492433852 0.27172003795638644 chr18 78077248 3260633 0.041761628176239 0.5732353015916273 chr19 59128983 2702143 0.04569912863206188 0.5424004601691048 chr20 63025520 3029968 0.04807525586460849 0.2536581777058664 chr21 48129895 2343868 0.04869879728596956 0.2634735849904838 chr22 51304566 1434765 0.027965639549509102 0.1859159496728531 chrMT 16571 300477 18.132701707802788 10.565652429982313 chrX 155270560 7348081 0.04732436722067596 0.273663517907178 chrY 59373566 313927 0.005287319276056284 0.11262102281114132