BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081057.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 = 2,476,340 number of mapped reads = 2,232,026 (90.13%) number of supplementary alignments = 24,678 (1%) number of secondary alignments = 0 number of mapped bases = 149,878,200 bp number of sequenced bases = 149,823,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,671 duplication rate = 3.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6864 >>>>>>> ACTG content number of A's = 41,535,023 bp (27.72%) number of C's = 28,434,413 bp (18.98%) number of T's = 46,736,191 bp (31.19%) number of G's = 33,116,746 bp (22.1%) number of N's = 1,610 bp (0%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,356,108 number of insertions = 11,828 mapped reads with insertion percentage = 0.52% number of deletions = 32,984 mapped reads with deletion percentage = 1.46% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.3907X There is a 3.95% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11852037 0.047550681929895776 0.5715918879530882 chr2 243199373 11335172 0.046608557662687726 0.4383906362467808 chr3 198022430 13255313 0.06693844227646333 0.30502915217038395 chr4 191154276 8708641 0.04555818045106142 0.2745336363334006 chr5 180915260 8137737 0.04498093195676252 0.24884137534875853 chr6 171115067 12968364 0.07578738814390903 0.48949108757036586 chr7 159138663 7359073 0.046243149598410284 0.3743269677387614 chr8 146364022 10251205 0.07003910428206188 0.4609009104393271 chr9 141213431 7601947 0.053833030938820546 0.4552605786958818 chr10 135534747 6663937 0.04916773851357837 0.38782026966679595 chr11 135006516 7225708 0.05352117967402403 0.34190860270913376 chr12 133851895 7354216 0.05494293524944118 0.288968691225775 chr13 115169878 3913813 0.03398295689780969 0.2160787572221458 chr14 107349540 4301776 0.04007260767023315 0.29935383064343946 chr15 102531392 3303530 0.03221969326233277 0.21161518527316578 chr16 90354753 3424973 0.03790584209775882 0.2824100999561238 chr17 81195210 3366315 0.041459526984412014 0.25356644602720724 chr18 78077248 3680642 0.047141031405205265 0.7877206882332072 chr19 59128983 2904063 0.04911403600498253 0.417545430308689 chr20 63025520 2246171 0.035639071284140136 0.2378857355484166 chr21 48129895 3509104 0.07290903086325037 0.3599076089902135 chr22 51304566 1296235 0.025265490015060257 0.1849582318884703 chrMT 16571 471702 28.46551203910446 13.330445213958857 chrX 155270560 4349636 0.02801326922502244 0.2312374981077102 chrY 59373566 396890 0.006684624602133549 0.178857799845718