BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234116.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 = 845,579 number of mapped reads = 597,610 (70.67%) number of supplementary alignments = 2,561 (0.3%) number of secondary alignments = 0 number of mapped bases = 39,375,848 bp number of sequenced bases = 39,354,602 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,278 duplication rate = 1.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4361 >>>>>>> ACTG content number of A's = 11,152,243 bp (28.34%) number of C's = 6,766,003 bp (17.19%) number of T's = 12,619,313 bp (32.07%) number of G's = 8,809,919 bp (22.39%) number of N's = 7,124 bp (0.02%) GC percentage = 39.58% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 371,154 number of insertions = 3,460 mapped reads with insertion percentage = 0.57% number of deletions = 11,955 mapped reads with deletion percentage = 1.97% homopolymer indels = 46.1% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 0.1602X There is a 1.19% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3577196 0.014351803761403667 0.21835449945990446 chr2 243199373 2338274 0.009614638274581406 0.15343348594143238 chr3 198022430 4172321 0.02106994142027244 0.1521017125649865 chr4 191154276 1343048 0.007025989834514609 0.08917306846369255 chr5 180915260 3061549 0.016922558108144112 0.13557744045427694 chr6 171115067 2864566 0.016740583107155607 0.14344767467634395 chr7 159138663 2280752 0.014331853472967785 0.14835777608712986 chr8 146364022 928969 0.006346976444798709 0.359521709318796 chr9 141213431 1557963 0.011032682861448215 0.13345919113667667 chr10 135534747 781229 0.005764049568779584 0.09426937264831664 chr11 135006516 1224692 0.00907135474853673 0.1187945583432563 chr12 133851895 873698 0.006527348753635502 0.08502601313088808 chr13 115169878 2227303 0.019339284183317446 0.14528789754100335 chr14 107349540 2923563 0.027234052423512945 0.1758977491741284 chr15 102531392 749876 0.0073136235193217705 0.08956276914121514 chr16 90354753 1167950 0.012926270740843042 0.12797908385575385 chr17 81195210 1445954 0.017808365789065635 0.14358338885428537 chr18 78077248 1183658 0.015160088634271535 0.23172055977519265 chr19 59128983 988866 0.016723879725785238 0.1639891066237796 chr20 63025520 1230315 0.019520902009217852 0.14848175478754486 chr21 48129895 821802 0.017074668457099273 0.13937940983288422 chr22 51304566 738807 0.014400414185357303 0.12603070052109241 chrMT 16571 5809 0.35055216945265827 0.6514418887567143 chrX 155270560 811842 0.005228563611801232 0.08087250443660574 chrY 59373566 75846 0.001277437167914085 0.04349085171465318