BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708623.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 = 3,964,676 number of mapped reads = 2,873,155 (72.47%) number of supplementary alignments = 949 (0.02%) number of secondary alignments = 0 number of mapped bases = 139,721,353 bp number of sequenced bases = 139,694,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,187 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0436 >>>>>>> ACTG content number of A's = 41,071,934 bp (29.4%) number of C's = 26,210,038 bp (18.76%) number of T's = 44,330,631 bp (31.73%) number of G's = 28,069,896 bp (20.09%) number of N's = 11,931 bp (0.01%) GC percentage = 38.86% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 891,355 number of insertions = 6,492 mapped reads with insertion percentage = 0.23% number of deletions = 17,641 mapped reads with deletion percentage = 0.61% homopolymer indels = 48.1% >>>>>>> Coverage mean coverageData = 0.0451X std coverageData = 0.4566X There is a 3.72% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% 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 10606159 0.04255218686095069 0.784651044559594 chr2 243199373 12304656 0.05059493307164077 0.48036395007426014 chr3 198022430 9598747 0.04847302904019509 0.2624153797777617 chr4 191154276 9491432 0.04965325494471282 0.26771980584154803 chr5 180915260 8805985 0.04867463916531972 0.26746091393338156 chr6 171115067 8293379 0.04846667885768353 0.35102737932866146 chr7 159138663 8135284 0.051120726080248646 0.7408121033016153 chr8 146364022 7576353 0.05176376609820137 0.8408144690092754 chr9 141213431 5883493 0.041663834369975755 0.35845864191218757 chr10 135534747 6407343 0.0472745413395725 0.3578135442250427 chr11 135006516 6347501 0.047016256607940315 0.3772476926562629 chr12 133851895 6376906 0.047641507055241915 0.2702097160352889 chr13 115169878 4916477 0.04268891384950499 0.2517975041002955 chr14 107349540 4135623 0.0385248320579669 0.2600615898725022 chr15 102531392 3731273 0.036391518024060376 0.22475181391326865 chr16 90354753 3391498 0.03753535799051988 0.24779783632082067 chr17 81195210 3264663 0.040207581210763545 0.28310511051111115 chr18 78077248 4011334 0.05137647781848049 0.7331315080071398 chr19 59128983 2260489 0.03822979671407506 0.5957179227877435 chr20 63025520 2711233 0.043018018732729216 0.2509078808737145 chr21 48129895 1879224 0.039044838971703556 0.24959209779155533 chr22 51304566 1281618 0.024980583599518217 0.183403882624251 chrMT 16571 11942 0.720656568704363 1.143600478306041 chrX 155270560 7988124 0.05144648154807969 0.31152654496518606 chrY 59373566 310617 0.005231570561215744 0.09503215557175859