BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063555.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 = 2,780,061 number of mapped reads = 2,529,307 (90.98%) number of supplementary alignments = 21,838 (0.79%) number of secondary alignments = 0 number of mapped bases = 167,240,801 bp number of sequenced bases = 167,166,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 152,388 duplication rate = 4.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2719 >>>>>>> ACTG content number of A's = 46,584,948 bp (27.87%) number of C's = 30,385,209 bp (18.18%) number of T's = 53,476,043 bp (31.99%) number of G's = 36,716,601 bp (21.96%) number of N's = 4,138 bp (0%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,345,825 number of insertions = 12,340 mapped reads with insertion percentage = 0.48% number of deletions = 45,352 mapped reads with deletion percentage = 1.77% homopolymer indels = 46.7% >>>>>>> Coverage mean coverageData = 0.054X std coverageData = 0.5688X There is a 4.17% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 15868891 0.06366640506785337 1.042507775130384 chr2 243199373 8216715 0.03378592180827703 0.5195203328416113 chr3 198022430 12808935 0.0646842632927997 0.3117527388433571 chr4 191154276 18700749 0.09783066008944524 0.39402990941775545 chr5 180915260 8640148 0.04775798348906554 0.2714347512161138 chr6 171115067 2934549 0.01714956521040897 0.21726035777663 chr7 159138663 19511921 0.12260955717593279 1.159947128288211 chr8 146364022 10211726 0.06976937269460934 1.0348181929415246 chr9 141213431 1186418 0.008401594604694506 0.36198051511138635 chr10 135534747 7569003 0.05584547997865079 0.461259266539499 chr11 135006516 6815291 0.05048120047776064 0.3402262120474643 chr12 133851895 12283949 0.09177269399137009 0.3999270334112529 chr13 115169878 1180077 0.010246403143710893 0.1343850399696086 chr14 107349540 7771481 0.07239417141424173 0.37564113250394504 chr15 102531392 2809584 0.027402183323523004 0.21545204201141677 chr16 90354753 7321493 0.08103052420496351 0.3660657521394221 chr17 81195210 3881429 0.04780366969923472 0.27452621251977494 chr18 78077248 5981524 0.07661033339699679 0.7224653473423587 chr19 59128983 3534861 0.05978220528501226 0.781735459628665 chr20 63025520 1412541 0.022412206991707487 0.22197806843488702 chr21 48129895 2587867 0.05376839072680296 0.287251836936073 chr22 51304566 593656 0.011571211809880626 0.12575762102833718 chrMT 16571 54917 3.3140426045501177 3.0087592465321067 chrX 155270560 5128421 0.03302893349518415 0.2640879659478914 chrY 59373566 234655 0.003952179661905434 0.07953910352155695