BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708576.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,836,285 number of mapped reads = 3,167,555 (82.57%) number of supplementary alignments = 83 (0%) number of secondary alignments = 0 number of mapped bases = 157,966,058 bp number of sequenced bases = 157,951,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,695 duplication rate = 0.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5739 >>>>>>> ACTG content number of A's = 48,942,049 bp (30.99%) number of C's = 30,013,464 bp (19%) number of T's = 48,668,645 bp (30.81%) number of G's = 30,320,136 bp (19.2%) number of N's = 7,473 bp (0%) GC percentage = 38.2% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 248,368 number of insertions = 10,703 mapped reads with insertion percentage = 0.34% number of deletions = 8,466 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.2326X There is a 4.84% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 12866027 0.051618836287673685 0.23448254524911122 chr2 243199373 14046779 0.057758286243608035 0.24697846499542306 chr3 198022430 12150519 0.061359306619962195 0.2543085777176891 chr4 191154276 12174614 0.06368999038242806 0.25942355115167665 chr5 180915260 10726415 0.05928971939680489 0.24976997330780665 chr6 171115067 9855615 0.0575964184381262 0.2463160379940847 chr7 159138663 8168203 0.05132758341698523 0.23248961753945704 chr8 146364022 8583176 0.05864266288063606 0.24843875178308403 chr9 141213431 6275215 0.04443780563620751 0.21733385374116856 chr10 135534747 6736585 0.04970374866306424 0.2283118417110119 chr11 135006516 7691557 0.05697174646000049 0.2461931354557079 chr12 133851895 7674051 0.057332404595392544 0.24664549325623342 chr13 115169878 5337746 0.04634671923504165 0.22190830429822744 chr14 107349540 4409665 0.041077632936293906 0.20850171922473285 chr15 102531392 4339322 0.04232188713482014 0.2123473980616251 chr16 90354753 2862462 0.03168025925542622 0.18242917141987158 chr17 81195210 2749429 0.03386196057624582 0.1898273754819434 chr18 78077248 4726291 0.06053352443979583 0.2528950508276638 chr19 59128983 1412010 0.02388016719313437 0.15807427809969773 chr20 63025520 2491827 0.039536793984405044 0.2041988807240644 chr21 48129895 1716290 0.0356595417463512 0.19522359273775627 chr22 51304566 894933 0.01744353514266157 0.1353660746650021 chrMT 16571 300 0.018103916480598635 0.13332728411192565 chrX 155270560 9841026 0.06337985771417325 0.25948773381921997 chrY 59373566 236001 0.0039748496831064515 0.06493829460288401