BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006416.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 12,967,514 number of mapped reads = 11,693,816 (90.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,894,094 number of mapped paired reads (second in pair) = 5,799,722 number of mapped paired reads (both in pair) = 10,896,254 number of mapped paired reads (singletons) = 797,562 number of mapped bases = 452,849,225 bp number of sequenced bases = 452,794,993 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 629,722 duplication rate = 4.53% >>>>>>> Insert size mean insert size = 61,067.6562 std insert size = 2,343,570.742 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 48.5661 >>>>>>> ACTG content number of A's = 127,738,777 bp (28.21%) number of C's = 96,480,190 bp (21.31%) number of T's = 129,820,140 bp (28.67%) number of G's = 98,736,946 bp (21.81%) number of N's = 18,940 bp (0%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 1,766,486 number of insertions = 12,239 mapped reads with insertion percentage = 0.1% number of deletions = 41,153 mapped reads with deletion percentage = 0.35% homopolymer indels = 44.76% >>>>>>> Coverage mean coverageData = 0.1463X std coverageData = 0.7744X There is a 11.04% of reference with a coverageData >= 1X There is a 2.45% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 37497746 0.1504419361105624 1.0835795816493248 chr2 243199373 38387732 0.15784469970652432 0.7028325186700941 chr3 198022430 30532073 0.15418492238480258 0.4860688936968381 chr4 191154276 28546698 0.14933852696028627 0.592052544319853 chr5 180915260 27170374 0.1501828756733954 0.48629027882643816 chr6 171115067 25250556 0.14756477289051348 0.5442247287465085 chr7 159138663 23298516 0.14640386918419693 0.8450010088059938 chr8 146364022 23717214 0.16204265007147728 1.8933070758557906 chr9 141213431 19348890 0.13701876558753112 0.5965917932152763 chr10 135534747 22387760 0.16518096278292385 0.8416101840029439 chr11 135006516 21424313 0.15869095533137081 0.6594344045914986 chr12 133851895 20469794 0.15292868285503167 0.4960099215388018 chr13 115169878 13607561 0.11815208313409865 0.42972823143106986 chr14 107349540 14153328 0.1318433968138103 0.5057574331704234 chr15 102531392 12652355 0.12339981690680646 0.43644937817985024 chr16 90354753 13284164 0.14702230440494923 0.640468426299486 chr17 81195210 12354987 0.15216398849143933 0.5327390184253359 chr18 78077248 11789113 0.15099293714860443 1.0302656217538335 chr19 59128983 8780422 0.14849607678860297 0.8105213929557785 chr20 63025520 10367568 0.16449793670881255 0.5360648844317945 chr21 48129895 5569351 0.11571500415697977 0.5605618704480521 chr22 51304566 5530939 0.10780597968609655 0.42650485558287815 chrMT 16571 6543 0.39484641844185625 0.8320245146386521 chrX 155270560 25512046 0.16430703927389712 0.5733976861913961 chrY 59373566 1209182 0.0203656623892188 0.5030703257060779