BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240180.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 = 1,615,911 number of mapped reads = 1,255,321 (77.69%) number of supplementary alignments = 11,507 (0.71%) number of secondary alignments = 0 number of mapped bases = 83,252,626 bp number of sequenced bases = 83,214,206 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 128,997 duplication rate = 8.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0642 >>>>>>> ACTG content number of A's = 24,074,895 bp (28.93%) number of C's = 15,669,311 bp (18.83%) number of T's = 26,008,359 bp (31.25%) number of G's = 17,398,635 bp (20.91%) number of N's = 63,006 bp (0.08%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 748,647 number of insertions = 5,786 mapped reads with insertion percentage = 0.46% number of deletions = 22,196 mapped reads with deletion percentage = 1.75% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 0.0269X std coverageData = 0.3478X There is a 1.44% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 6596536 0.026465474683812322 0.46941471882206376 chr2 243199373 8929160 0.03671539070949825 0.3720664594425779 chr3 198022430 5136307 0.02593800611375186 0.27112932485851593 chr4 191154276 5646302 0.02953793196862622 0.5075538187603504 chr5 180915260 4398600 0.0243130402598432 0.2637618673373012 chr6 171115067 4287072 0.025053737669985542 0.27840578780324426 chr7 159138663 4970224 0.03123203316091703 0.47444855345492487 chr8 146364022 4760578 0.03252560250086596 0.4099989833277374 chr9 141213431 3092957 0.02190271122298558 0.3028142034936455 chr10 135534747 3868996 0.028546155769191794 0.3263393534944731 chr11 135006516 3566085 0.02641416952052892 0.3167922382060658 chr12 133851895 4489566 0.033541295773212625 0.31151376891679033 chr13 115169878 2168175 0.018825886053295986 0.23021382045513153 chr14 107349540 2621836 0.02442335570324754 0.27074375062447154 chr15 102531392 2299404 0.022426341388206258 0.25828992542424606 chr16 90354753 2419988 0.02678318427808662 0.2779694459844034 chr17 81195210 1955899 0.02408884711302551 0.2770468015738234 chr18 78077248 1986644 0.02544459558820516 0.45095761632617876 chr19 59128983 1450040 0.02452333739614632 0.34219949602498195 chr20 63025520 1629336 0.02585200407707862 0.26595607944526684 chr21 48129895 1344577 0.027936420804574785 0.28977214492914793 chr22 51304566 744209 0.01450570695793431 0.19670909938758208 chrMT 16571 12716 0.7673646732243076 1.6624014429004772 chrX 155270560 4640236 0.029884841015579516 0.299071043658937 chrY 59373566 237183 0.0039947575323334965 0.09735272179420033