BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716326.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 = 1,711,230 number of mapped reads = 1,548,129 (90.47%) number of supplementary alignments = 8,973 (0.52%) number of secondary alignments = 0 number of mapped bases = 90,069,764 bp number of sequenced bases = 90,044,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,021 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1187 >>>>>>> ACTG content number of A's = 23,408,394 bp (26%) number of C's = 16,735,665 bp (18.59%) number of T's = 27,621,484 bp (30.68%) number of G's = 22,276,721 bp (24.74%) number of N's = 2,542 bp (0%) GC percentage = 43.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 454,482 number of insertions = 6,127 mapped reads with insertion percentage = 0.39% number of deletions = 16,066 mapped reads with deletion percentage = 1.03% homopolymer indels = 40.81% >>>>>>> Coverage mean coverageData = 0.0291X std coverageData = 0.2689X There is a 2.62% of reference with a coverageData >= 1X There is a 0.21% 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 9108014 0.036541590000692514 0.473895621229859 chr2 243199373 6879338 0.02828682457170644 0.29638037374117265 chr3 198022430 8105703 0.04093325690428099 0.22169488756588898 chr4 191154276 4330626 0.022655135373482307 0.1737251835068293 chr5 180915260 4436546 0.024522784866240693 0.17398819023834097 chr6 171115067 7416031 0.04333943895191883 0.3238297056492239 chr7 159138663 3615695 0.02272040578850408 0.2559991220234637 chr8 146364022 6804014 0.04648692969095916 0.26129774548472817 chr9 141213431 3784134 0.026797266897367573 0.2569329333590871 chr10 135534747 4586299 0.033838547689914525 0.2987020235864795 chr11 135006516 4457057 0.03301364357850698 0.26961397236090684 chr12 133851895 4313884 0.032228785404943276 0.20275465642846857 chr13 115169878 2091608 0.018161068122343586 0.14656959988956608 chr14 107349540 1964334 0.018298485489551236 0.18822612933667465 chr15 102531392 1857043 0.01811194565660437 0.15171136088423529 chr16 90354753 1901775 0.02104786894829982 0.1814886933918644 chr17 81195210 1466308 0.01805904560133535 0.15653309843191882 chr18 78077248 1025199 0.013130572942325017 0.4228180109861537 chr19 59128983 1692626 0.028625995478393396 0.34979397569071546 chr20 63025520 1366868 0.021687532288507894 0.16063506529653337 chr21 48129895 815505 0.01694383501148299 0.16768259508685046 chr22 51304566 1429817 0.027869195891843234 0.18094395785929682 chrMT 16571 39046 2.3562850763381813 1.8887601219124392 chrX 155270560 6359120 0.04095509155116076 0.25511470922951396 chrY 59373566 223174 0.0037588107812153307 0.08580659835043247