BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085113.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,428,511 number of mapped reads = 2,204,925 (90.79%) number of supplementary alignments = 22,482 (0.93%) number of secondary alignments = 0 number of mapped bases = 146,013,235 bp number of sequenced bases = 145,959,602 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,881 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3631 >>>>>>> ACTG content number of A's = 40,846,522 bp (27.98%) number of C's = 27,030,611 bp (18.52%) number of T's = 45,523,743 bp (31.19%) number of G's = 32,539,114 bp (22.29%) number of N's = 19,612 bp (0.01%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,226,026 number of insertions = 11,566 mapped reads with insertion percentage = 0.52% number of deletions = 33,621 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.0472X std coverageData = 0.4727X There is a 4.23% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 11736940 0.04708890976042945 1.0078037008130898 chr2 243199373 12304288 0.050593419909844915 0.5392177480996244 chr3 198022430 10005222 0.05052570054816517 0.24600218268372218 chr4 191154276 9979199 0.05220494779829042 0.25727887936211696 chr5 180915260 9347407 0.05166732203795302 0.2488444062659337 chr6 171115067 8579024 0.050135994161168755 0.3622578438053268 chr7 159138663 8115563 0.05099680270658049 0.42679045720343556 chr8 146364022 7681625 0.05248301389258079 0.5913112944750764 chr9 141213431 6151382 0.04356088479997345 0.41577680071381873 chr10 135534747 6798533 0.05016081226757298 0.49728262500642 chr11 135006516 6727608 0.04983172812192265 0.43465173425979153 chr12 133851895 6607323 0.049362939538510085 0.24724929674865537 chr13 115169878 4575517 0.03972841752945158 0.2140778542014511 chr14 107349540 4189855 0.03903002285803926 0.24850134664471563 chr15 102531392 3904083 0.0380769530564844 0.21684620284032635 chr16 90354753 3846412 0.04257011249867508 0.28388603561466474 chr17 81195210 3663758 0.04512283421645193 0.29296677837264046 chr18 78077248 4030045 0.05161612509703211 0.8249144594664963 chr19 59128983 2492525 0.04215403129798461 0.6948374733792041 chr20 63025520 2857190 0.04533385841164024 0.2448035817147391 chr21 48129895 1909196 0.03966757043621225 0.2368622337921359 chr22 51304566 1450342 0.028269257749885264 0.17896316876370041 chrMT 16571 38992 2.3530263713716733 1.9424001839684315 chrX 155270560 8662705 0.0557910334064616 0.31688334623264786 chrY 59373566 358501 0.0060380574075675365 0.13082706233485658