BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617364.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,643,063 (92.63%) number of supplementary alignments = 67,898 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,940,884 number of mapped paired reads (second in pair) = 14,702,179 number of mapped paired reads (both in pair) = 28,951,346 number of mapped paired reads (singletons) = 691,717 number of mapped bases = 2,904,218,868 bp number of sequenced bases = 2,903,375,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,518,532 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 48,934.8142 std insert size = 2,088,653.7485 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.3917 >>>>>>> ACTG content number of A's = 880,467,947 bp (30.33%) number of C's = 575,892,838 bp (19.84%) number of T's = 866,533,429 bp (29.85%) number of G's = 578,940,608 bp (19.94%) number of N's = 1,540,321 bp (0.05%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0134 number of mismatches = 38,101,505 number of insertions = 290,522 mapped reads with insertion percentage = 0.95% number of deletions = 352,826 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.22% >>>>>>> Coverage mean coverageData = 0.9381X std coverageData = 9.5755X There is a 52.21% of reference with a coverageData >= 1X There is a 23.4% of reference with a coverageData >= 2X There is a 8.95% of reference with a coverageData >= 3X There is a 3.14% of reference with a coverageData >= 4X There is a 1.08% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% 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 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 188638437 0.7568223350584952 19.66841457085605 chr2 243199373 286446678 1.1778265480972272 8.55624530053625 chr3 198022430 231323478 1.1681680605575844 1.4872996786946031 chr4 191154276 159334335 0.8335379063139555 8.880726305362897 chr5 180915260 182554743 1.0090621598200173 1.4473359650461117 chr6 171115067 136535730 0.7979176374924366 3.6071040950176356 chr7 159138663 235964857 1.4827625955359447 10.665242654522386 chr8 146364022 122497854 0.8369396544732831 7.336321525685596 chr9 141213431 122218987 0.8654912364532804 14.328587951053867 chr10 135534747 122458317 0.9035197225107153 19.92725633192703 chr11 135006516 155831969 1.1542551694319703 5.445219531301841 chr12 133851895 128274056 0.9583282776833305 1.365662062155722 chr13 115169878 127055610 1.1032017416915212 1.2846730905177286 chr14 107349540 83820761 0.7808208679794995 1.3348545496443358 chr15 102531392 65057977 0.6345176411922702 0.9683998942259171 chr16 90354753 72500164 0.8023945790654754 7.855974427814433 chr17 81195210 89949274 1.1078150299752905 7.040371135370534 chr18 78077248 52511636 0.6725600267058593 14.762951871686633 chr19 59128983 53514579 0.9050481893118304 9.305855845188349 chr20 63025520 83112882 1.3187179098244648 2.3781502546687205 chr21 48129895 46246251 0.9608633262133649 3.0902140895954915 chr22 51304566 25507647 0.4971808357174291 0.8994331124741877 chrMT 16571 1980775 119.53261722285922 20.338210410083178 chrX 155270560 121175148 0.7804128999083921 2.9145350218629114 chrY 59373566 9706723 0.16348559896166587 7.832056794656204