BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004028.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 = 1,744,429 number of mapped reads = 1,508,440 (86.47%) number of supplementary alignments = 19,116 (1.1%) number of secondary alignments = 0 number of mapped bases = 100,045,659 bp number of sequenced bases = 99,986,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,114 duplication rate = 5.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.729 >>>>>>> ACTG content number of A's = 28,308,900 bp (28.31%) number of C's = 18,175,537 bp (18.18%) number of T's = 32,192,715 bp (32.2%) number of G's = 21,292,425 bp (21.3%) number of N's = 16,566 bp (0.02%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 972,502 number of insertions = 7,989 mapped reads with insertion percentage = 0.52% number of deletions = 34,969 mapped reads with deletion percentage = 2.28% homopolymer indels = 44.63% >>>>>>> Coverage mean coverageData = 0.0323X std coverageData = 0.3896X There is a 2.42% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 10290623 0.04128624818952808 0.8413921359513354 chr2 243199373 12820595 0.05271639824499054 0.44819741349999337 chr3 198022430 5985520 0.030226474849339036 0.22416147347683185 chr4 191154276 8245837 0.04313707845070649 0.28294285090432003 chr5 180915260 7790698 0.04306269133958075 0.2658122279123171 chr6 171115067 1144056 0.006685886988549056 0.10686516904474516 chr7 159138663 3860216 0.02425693371572438 0.3716000712998648 chr8 146364022 3030568 0.02070568954438817 0.3445356158083414 chr9 141213431 2623899 0.01858108666731566 0.29316818019013063 chr10 135534747 4719367 0.034820347582159135 0.44766931153915507 chr11 135006516 6780520 0.05022364994590335 0.4476092831014286 chr12 133851895 7472019 0.05582303485505379 0.30484254701722685 chr13 115169878 5874801 0.051009874300639614 0.2868148259690441 chr14 107349540 1035838 0.009649207625854755 0.1486855191187696 chr15 102531392 3366196 0.03283088168743481 0.23129425183768929 chr16 90354753 2243505 0.024829961075761006 0.22610267022728517 chr17 81195210 2444528 0.03010680063516062 0.26495845033138565 chr18 78077248 4373102 0.05600994030937156 0.5707842387420774 chr19 59128983 650635 0.011003656193444084 0.5788040313037042 chr20 63025520 2369606 0.03759756365358033 0.2500630195210319 chr21 48129895 704702 0.014641669174636678 0.19457135051089916 chr22 51304566 679890 0.013252036865490686 0.1413766894667515 chrMT 16571 53064 3.202220747088287 2.985398572840804 chrX 155270560 1255563 0.0080862914386346 0.17092466825313343 chrY 59373566 230311 0.003879015789619239 0.13757844591866814