BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716704.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,671,634 number of mapped reads = 1,498,398 (89.64%) number of supplementary alignments = 5,312 (0.32%) number of secondary alignments = 0 number of mapped bases = 85,723,332 bp number of sequenced bases = 85,698,347 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,568 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5493 >>>>>>> ACTG content number of A's = 21,091,399 bp (24.61%) number of C's = 18,032,175 bp (21.04%) number of T's = 25,599,250 bp (29.87%) number of G's = 20,974,870 bp (24.48%) number of N's = 653 bp (0%) GC percentage = 45.52% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 444,436 number of insertions = 6,043 mapped reads with insertion percentage = 0.4% number of deletions = 15,819 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.11% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2313X There is a 2.52% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% 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 7370443 0.02957040977643141 0.27107410932929155 chr2 243199373 6871352 0.02825398731599526 0.33996889562387095 chr3 198022430 5058901 0.025547111001516343 0.17442649022826848 chr4 191154276 5313945 0.027799247347205562 0.18954686894025324 chr5 180915260 4980974 0.02753208325267863 0.1778141419285779 chr6 171115067 4723449 0.027603933907234483 0.21113438471902057 chr7 159138663 5002368 0.031434020530887584 0.34146438821824454 chr8 146364022 4537794 0.031003479803253835 0.22209535362792007 chr9 141213431 2937741 0.020803552319325774 0.17835529209268394 chr10 135534747 3826477 0.028232442858361628 0.2817739419717512 chr11 135006516 3101499 0.022972957838568325 0.20634087292529046 chr12 133851895 4409255 0.03294129679673194 0.19702335693022524 chr13 115169878 2672633 0.02320600704291794 0.16560558999429262 chr14 107349540 2934533 0.02733624196247138 0.18463395657120513 chr15 102531392 3208842 0.03129619073151762 0.19404920593859473 chr16 90354753 3022968 0.033456657227539544 0.20895088014789479 chr17 81195210 3947116 0.04861267062428929 0.25067217521897006 chr18 78077248 1623340 0.020791460272780105 0.2703977008884717 chr19 59128983 1821904 0.030812368276315526 0.2682799293093136 chr20 63025520 1409737 0.022367717077145893 0.16660430652293431 chr21 48129895 1093887 0.02272780773778958 0.17190255426738804 chr22 51304566 805368 0.015697784091965615 0.13774681025333196 chrMT 16571 19303 1.1648663327499849 1.310155498905076 chrX 155270560 4777545 0.030769161906803195 0.2015924952005419 chrY 59373566 251958 0.004243605647671558 0.11115179770057673