BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238050.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 = 1,978,083 number of mapped reads = 1,732,942 (87.61%) number of supplementary alignments = 21,473 (1.09%) number of secondary alignments = 0 number of mapped bases = 114,844,429 bp number of sequenced bases = 114,787,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,972 duplication rate = 5.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.399 >>>>>>> ACTG content number of A's = 31,682,085 bp (27.6%) number of C's = 21,398,790 bp (18.64%) number of T's = 36,239,843 bp (31.57%) number of G's = 25,451,112 bp (22.17%) number of N's = 15,816 bp (0.01%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 893,476 number of insertions = 8,344 mapped reads with insertion percentage = 0.48% number of deletions = 32,092 mapped reads with deletion percentage = 1.83% homopolymer indels = 45.74% >>>>>>> Coverage mean coverageData = 0.0371X std coverageData = 0.3658X There is a 2.63% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 8263978 0.0331552955288324 0.30377381709800244 chr2 243199373 16385689 0.06737553965651054 0.46370594129691556 chr3 198022430 11315941 0.0571447436535346 0.31861601923396426 chr4 191154276 10207022 0.05339677570173738 0.3419372221664713 chr5 180915260 6879023 0.038023453632380154 0.26205082240561367 chr6 171115067 2104620 0.012299442923982842 0.16003715760550316 chr7 159138663 10684588 0.06714011415315209 0.7061841972865817 chr8 146364022 9794152 0.06691639014948633 0.6553927614647307 chr9 141213431 7323408 0.05186056275341118 0.41478702146401114 chr10 135534747 986098 0.007275610290547855 0.27894739551593317 chr11 135006516 748630 0.005545139761994895 0.1499171905290889 chr12 133851895 910974 0.006805835658882528 0.12669899367406448 chr13 115169878 3503661 0.030421678487842108 0.23132949992066967 chr14 107349540 2726009 0.025393765078080447 0.26931400640254827 chr15 102531392 4922931 0.04801389022398135 0.293956423844496 chr16 90354753 907524 0.010044009527644882 0.18820092645772654 chr17 81195210 1277554 0.01573435181705916 0.17549022987556367 chr18 78077248 895145 0.011464863618143918 0.638817704331408 chr19 59128983 1415813 0.023944484213435566 0.28584248741707685 chr20 63025520 1867159 0.02962544378848441 0.23850409777143705 chr21 48129895 379900 0.007893223120474292 0.2076975992904385 chr22 51304566 1101015 0.021460370603271453 0.1918912390622646 chrMT 16571 16711 1.0084484943576126 1.4796731385216648 chrX 155270560 9856714 0.06348089425323127 0.35898573724366073 chrY 59373566 370170 0.006234592680520486 0.223684233977229