BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708580.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 = 4,988,837 number of mapped reads = 4,903,381 (98.29%) number of supplementary alignments = 138 (0%) number of secondary alignments = 0 number of mapped bases = 244,569,138 bp number of sequenced bases = 244,548,087 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,358 duplication rate = 0.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7289 >>>>>>> ACTG content number of A's = 75,762,873 bp (30.98%) number of C's = 46,330,503 bp (18.95%) number of T's = 75,448,889 bp (30.85%) number of G's = 46,996,798 bp (19.22%) number of N's = 9,024 bp (0%) GC percentage = 38.16% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 351,978 number of insertions = 15,182 mapped reads with insertion percentage = 0.31% number of deletions = 12,328 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.91% >>>>>>> Coverage mean coverageData = 0.079X std coverageData = 0.2942X There is a 7.27% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.05% 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 18515753 0.07428568452794346 0.2867963786190417 chr2 243199373 20626603 0.08481355336388964 0.30302607770270634 chr3 198022430 19655261 0.09925775075076092 0.3284734351865081 chr4 191154276 19470415 0.10185707276566494 0.3318631692749635 chr5 180915260 16088451 0.08892810368788127 0.3102137011133665 chr6 171115067 15786239 0.09225510807882277 0.31661243953674084 chr7 159138663 13410906 0.08427182777072847 0.3037875875202497 chr8 146364022 13363615 0.0913039612972647 0.3145981024781674 chr9 141213431 10336534 0.07319795239590206 0.2835052505578959 chr10 135534747 10470572 0.07725378348918893 0.2892758775958955 chr11 135006516 11847007 0.08775137194118839 0.31078053131096894 chr12 133851895 11168856 0.0834418967322054 0.3015045729367682 chr13 115169878 9498805 0.08247647010618522 0.3005811644195206 chr14 107349540 7797023 0.07263210443193328 0.2832847453385331 chr15 102531392 7092955 0.06917837417051745 0.2771452712420259 chr16 90354753 4316852 0.0477767008006762 0.22719968801429832 chr17 81195210 4137733 0.05096030911183061 0.23571210720043712 chr18 78077248 6864314 0.08791695629436119 0.3086426500270052 chr19 59128983 2013897 0.034059388438999534 0.19122888080216788 chr20 63025520 3639054 0.05773937287625711 0.25113270015250083 chr21 48129895 2484947 0.05163001082798955 0.2388019494615509 chr22 51304566 1267505 0.024705500871014092 0.16298571638621964 chrMT 16571 550 0.033190513547764165 0.1791337582874871 chrX 155270560 14389293 0.0926723842562299 0.3182724465563733 chrY 59373566 325998 0.005490625238847874 0.0776594825233791