BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013189.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 = 2,437,019 number of mapped reads = 2,172,953 (89.16%) number of supplementary alignments = 17,123 (0.7%) number of secondary alignments = 0 number of mapped bases = 139,114,083 bp number of sequenced bases = 139,056,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,043 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7871 >>>>>>> ACTG content number of A's = 37,387,609 bp (26.89%) number of C's = 26,906,875 bp (19.35%) number of T's = 41,763,796 bp (30.03%) number of G's = 32,982,139 bp (23.72%) number of N's = 15,594 bp (0.01%) GC percentage = 43.07% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,090,762 number of insertions = 10,559 mapped reads with insertion percentage = 0.48% number of deletions = 34,093 mapped reads with deletion percentage = 1.55% homopolymer indels = 43.65% >>>>>>> Coverage mean coverageData = 0.0449X std coverageData = 0.4909X There is a 4.03% of reference with a coverageData >= 1X There is a 0.29% 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 0.01% 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 8403664 0.03371571940837812 0.7703111780988621 chr2 243199373 14102254 0.057986391272480786 0.6968332123699681 chr3 198022430 12530904 0.06328022537648892 0.27027415148760653 chr4 191154276 8274778 0.04328847971990959 0.23926699326720183 chr5 180915260 6075135 0.03358000314622437 0.20331617186847997 chr6 171115067 8367963 0.04890254930034887 0.33880527458360116 chr7 159138663 8440734 0.05304012136887187 0.9743430964930406 chr8 146364022 9600417 0.06559273835751794 0.4655114282006543 chr9 141213431 4867490 0.034469030074058604 0.4944128305003811 chr10 135534747 5889826 0.04345620684266301 0.476177943028108 chr11 135006516 5154065 0.038176416610884174 0.3603039320049942 chr12 133851895 6187356 0.04622538963680716 0.24409068166617284 chr13 115169878 2887950 0.025075567067979355 0.1676519258749044 chr14 107349540 5138042 0.04786272954686159 0.27697242081388823 chr15 102531392 3088697 0.03012440326568472 0.21908414979864255 chr16 90354753 3968641 0.04392288029385682 0.28228269177132626 chr17 81195210 4812341 0.059268779525294656 0.31059623857723995 chr18 78077248 4210708 0.05393002581238519 0.9802682939845961 chr19 59128983 2871132 0.0485571010074704 0.6136729763643685 chr20 63025520 2757996 0.04375998801755226 0.2429350578335191 chr21 48129895 2149130 0.04465270493525905 0.24667633687249665 chr22 51304566 1945965 0.03792966497367895 0.20880847135665087 chrMT 16571 134734 8.130710276989921 5.293466003787857 chrX 155270560 6971738 0.04490057870596976 0.29672089393562523 chrY 59373566 282423 0.004756712776861002 0.11417820743019527