BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549055.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 42,771,430 number of mapped reads = 37,455,790 (87.57%) number of secondary alignments = 0 number of mapped bases = 1,482,393,556 bp number of sequenced bases = 1,482,243,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,061,913 duplication rate = 8.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9162 >>>>>>> ACTG content number of A's = 417,324,372 bp (28.15%) number of C's = 318,828,551 bp (21.51%) number of T's = 425,716,113 bp (28.72%) number of G's = 320,362,026 bp (21.61%) number of N's = 12,151 bp (0%) GC percentage = 43.12% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 3,898,918 number of insertions = 45,359 mapped reads with insertion percentage = 0.12% number of deletions = 112,968 mapped reads with deletion percentage = 0.3% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 0.4789X std coverageData = 3.7101X There is a 24.01% of reference with a coverageData >= 1X There is a 11.29% of reference with a coverageData >= 2X There is a 5.47% of reference with a coverageData >= 3X There is a 2.73% of reference with a coverageData >= 4X There is a 1.42% of reference with a coverageData >= 5X There is a 0.78% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 118215834 0.47428501291477226 5.869073401060678 chr2 243199373 127349213 0.5236412060980108 2.5905392423482194 chr3 198022430 102686277 0.5185588167966629 1.2164682506686044 chr4 191154276 98408244 0.5148105815848975 1.4831701842344034 chr5 180915260 94103128 0.5201503068342604 1.262159965520121 chr6 171115067 89198911 0.5212802856220721 1.442728114216965 chr7 159138663 86958320 0.546431133457493 4.7416804735925595 chr8 146364022 76645732 0.5236651121817355 11.480449923568077 chr9 141213431 63186008 0.44745041284352055 2.5440222217867974 chr10 135534747 70937959 0.5233931561476262 2.5050918154032025 chr11 135006516 69708808 0.5163366188932689 1.981932602742205 chr12 133851895 68301125 0.5102738739709288 1.330788794248608 chr13 115169878 46056875 0.3999038272837278 1.0433047580314936 chr14 107349540 44159747 0.41136410086154074 1.6181228650838801 chr15 102531392 42367312 0.4132130772202917 1.0949854394190948 chr16 90354753 41573118 0.46010991806927964 1.4811851347225078 chr17 81195210 40192743 0.49501372063696863 1.2879887888903718 chr18 78077248 39241068 0.5025928680273157 4.865871716225995 chr19 59128983 31013872 0.5245121838134778 5.542653103772241 chr20 63025520 31382448 0.4979323931004457 1.3510824384855005 chr21 48129895 18771357 0.3900145013821451 1.7322317489296788 chr22 51304566 16977916 0.3309240740872849 1.8556691671347076 chrMT 16571 126848 7.6548186591032525 7.885061887956925 chrX 155270560 51504864 0.3317104285577382 1.6281381039767595 chrY 59373566 13325829 0.22444043532773492 2.0246613618752227