BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231721.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,355,059 number of mapped reads = 878,766 (64.85%) number of supplementary alignments = 3,377 (0.25%) number of secondary alignments = 0 number of mapped bases = 53,168,050 bp number of sequenced bases = 53,130,561 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,376 duplication rate = 4.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5446 >>>>>>> ACTG content number of A's = 13,582,214 bp (25.56%) number of C's = 9,543,797 bp (17.96%) number of T's = 16,847,923 bp (31.71%) number of G's = 13,148,324 bp (24.75%) number of N's = 8,303 bp (0.02%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 494,056 number of insertions = 4,402 mapped reads with insertion percentage = 0.5% number of deletions = 21,262 mapped reads with deletion percentage = 2.38% homopolymer indels = 46.24% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 0.1849X There is a 1.46% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 4623141 0.01854816241360538 0.24195126333817407 chr2 243199373 3761948 0.015468576064133191 0.20765483893022624 chr3 198022430 4294483 0.021686851332952534 0.17029176281392186 chr4 191154276 2585385 0.01352512250366819 0.1405370516505102 chr5 180915260 3074906 0.016996388253815626 0.15310311483396472 chr6 171115067 3366049 0.01967126015852245 0.1899874596887431 chr7 159138663 3234741 0.020326556344136184 0.25293505041936354 chr8 146364022 2573802 0.017584936276211376 0.19451033036270707 chr9 141213431 2140586 0.01515851562306421 0.17416104980732589 chr10 135534747 2636511 0.01945265740600084 0.17925554899672405 chr11 135006516 2489182 0.01843749526874688 0.19433312421666435 chr12 133851895 2135692 0.015955635144351152 0.14721580283076652 chr13 115169878 1909885 0.016583198950683962 0.16459409656305082 chr14 107349540 2177092 0.020280403623527406 0.1713968244106358 chr15 102531392 1306979 0.012747110660508735 0.13808073035987478 chr16 90354753 1545562 0.017105486415307892 0.15689114736538506 chr17 81195210 1512035 0.018622219217118843 0.16912792855789316 chr18 78077248 1231447 0.015772161949150668 0.2526720549795553 chr19 59128983 1491769 0.025229065752745992 0.2247928174137795 chr20 63025520 1271781 0.02017882597398641 0.17447627318084954 chr21 48129895 806159 0.016749652165249894 0.15358917095216018 chr22 51304566 566516 0.011042214059465974 0.12061421856696726 chrMT 16571 40887 2.467382777140788 3.3001392901980036 chrX 155270560 2179980 0.014039879807221664 0.14495794223829903 chrY 59373566 211532 0.003562730256087364 0.0751607283472789