BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082321.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 = 2,122,816 number of mapped reads = 1,902,057 (89.6%) number of supplementary alignments = 16,185 (0.76%) number of secondary alignments = 0 number of mapped bases = 127,789,180 bp number of sequenced bases = 127,743,458 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,786 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9771 >>>>>>> ACTG content number of A's = 35,720,038 bp (27.96%) number of C's = 23,809,352 bp (18.64%) number of T's = 39,917,084 bp (31.25%) number of G's = 28,294,430 bp (22.15%) number of N's = 2,554 bp (0%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,057,101 number of insertions = 10,167 mapped reads with insertion percentage = 0.53% number of deletions = 28,243 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.0413X std coverageData = 0.348X There is a 3.66% of reference with a coverageData >= 1X There is a 0.35% 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% 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 9947423 0.03990932082773026 0.5766555091633209 chr2 243199373 10858880 0.044650115113578026 0.4222122100678164 chr3 198022430 8843064 0.04465688053620996 0.23115407620160025 chr4 191154276 8709245 0.045561340202507426 0.23937218985077946 chr5 180915260 7247883 0.04006230872951237 0.22055476928401188 chr6 171115067 7627580 0.044575735694858475 0.2758238176154695 chr7 159138663 7132453 0.044819108477743085 0.42664145800904324 chr8 146364022 6733406 0.046004516055181924 0.5883502942507407 chr9 141213431 5347816 0.037870448739397884 0.31839469928353464 chr10 135534747 5888783 0.043448511399073186 0.3051807453808484 chr11 135006516 5864508 0.04343870335858456 0.29397163446035124 chr12 133851895 5905689 0.04412107127807193 0.23274476524496004 chr13 115169878 4244592 0.03685505336733968 0.210322213994326 chr14 107349540 3903803 0.03636534446258456 0.22331305119462425 chr15 102531392 3589874 0.0350124379468095 0.20915339155598617 chr16 90354753 3456037 0.038249642495287436 0.23545265895007345 chr17 81195210 3266154 0.04022594436297412 0.2399082033384479 chr18 78077248 3489415 0.04469182878986718 0.5576775131838906 chr19 59128983 2376368 0.040189563213018566 0.4488364195964378 chr20 63025520 2449586 0.038866573413436335 0.2208245586889257 chr21 48129895 1692226 0.03515956143266051 0.21618187814009554 chr22 51304566 1294420 0.025230113046858245 0.1726708227366166 chrMT 16571 5330 0.3216462494719691 0.6187203624170576 chrX 155270560 7608747 0.049003152947989626 0.2706264782598849 chrY 59373566 305898 0.005152090746915892 0.1047320852401144