BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237600.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 = 1,545,262 number of mapped reads = 1,255,253 (81.23%) number of supplementary alignments = 6,224 (0.4%) number of secondary alignments = 0 number of mapped bases = 78,878,593 bp number of sequenced bases = 78,832,687 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,061 duplication rate = 3.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.8026 >>>>>>> ACTG content number of A's = 20,188,452 bp (25.61%) number of C's = 14,441,848 bp (18.32%) number of T's = 24,104,971 bp (30.58%) number of G's = 20,040,151 bp (25.42%) number of N's = 57,265 bp (0.07%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 771,881 number of insertions = 7,444 mapped reads with insertion percentage = 0.59% number of deletions = 27,790 mapped reads with deletion percentage = 2.19% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.2779X There is a 2.1% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% 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% 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 6899231 0.027679894927924772 0.3618224906238219 chr2 243199373 6866615 0.028234509469726304 0.39541234585526874 chr3 198022430 5624570 0.02840370154027501 0.2122046357816631 chr4 191154276 4791927 0.02506837461485821 0.21799522979730265 chr5 180915260 4293776 0.023733630872265835 0.18954940458720787 chr6 171115067 4149860 0.024251867896589143 0.21140549885073157 chr7 159138663 4540554 0.028532060747550707 0.4121283727141017 chr8 146364022 4314485 0.0294777701585708 0.2671181994718825 chr9 141213431 3201030 0.022668027944169136 0.29822324312335363 chr10 135534747 3448960 0.02544705380975109 0.28441980827551233 chr11 135006516 3262643 0.024166559486654703 0.2973111701411382 chr12 133851895 4596999 0.03434392169046243 0.2408852109979834 chr13 115169878 2586501 0.022458137882198678 0.190582948458877 chr14 107349540 2135555 0.019893471364665374 0.21336246097881997 chr15 102531392 2274000 0.022178573368047124 0.19407195593900944 chr16 90354753 2056282 0.02275787306949973 0.21550959242055592 chr17 81195210 2032202 0.025028594667099203 0.2179730810715673 chr18 78077248 2000469 0.025621663816839446 0.41796949405316547 chr19 59128983 1674222 0.028314743718829055 0.2947687599102404 chr20 63025520 1728584 0.027426731266953448 0.21262837840424373 chr21 48129895 1000565 0.02078884651628681 0.20078648658921883 chr22 51304566 850393 0.01657538629212846 0.16428410645744349 chrMT 16571 58724 3.543781304688914 3.4503253171061985 chrX 155270560 4180907 0.026926591879362062 0.22787636428855038 chrY 59373566 309539 0.005213414333240486 0.13801755043140376