BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716527.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 = 1,058,729 number of mapped reads = 997,253 (94.19%) number of supplementary alignments = 20,380 (1.92%) number of secondary alignments = 0 number of mapped bases = 78,954,068 bp number of sequenced bases = 78,919,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,586 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2175 >>>>>>> ACTG content number of A's = 20,431,653 bp (25.89%) number of C's = 15,014,140 bp (19.02%) number of T's = 23,866,002 bp (30.24%) number of G's = 19,601,861 bp (24.84%) number of N's = 5,464 bp (0.01%) GC percentage = 43.86% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 498,063 number of insertions = 6,544 mapped reads with insertion percentage = 0.65% number of deletions = 18,716 mapped reads with deletion percentage = 1.85% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.0255X std coverageData = 0.2736X There is a 2.3% of reference with a coverageData >= 1X There is a 0.17% 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 7617644 0.030562186643458753 0.5712482029564973 chr2 243199373 6372144 0.02620131755027181 0.282552850954613 chr3 198022430 4951679 0.025005647087554678 0.1694209913491378 chr4 191154276 5082346 0.026587665765844547 0.1982483589356514 chr5 180915260 4666858 0.025795822862040494 0.17317009122448107 chr6 171115067 4325684 0.025279386998691353 0.18201485711418827 chr7 159138663 4210223 0.026456317532339707 0.30517550098364316 chr8 146364022 3970003 0.027124172633080552 0.3042886584136508 chr9 141213431 3148265 0.02229437368461078 0.2238012154834468 chr10 135534747 3676697 0.02712733879231722 0.2624158722441284 chr11 135006516 4408233 0.03265200177449213 0.29774915303585703 chr12 133851895 3415653 0.025518151984325662 0.1711801710380427 chr13 115169878 2806837 0.024371277010469698 0.16764581965749684 chr14 107349540 2266638 0.021114557174627856 0.166556134705848 chr15 102531392 2213063 0.02158424807106881 0.1569874753718881 chr16 90354753 1721103 0.019048284045444737 0.15745307986507728 chr17 81195210 2470241 0.030423481877810278 0.21480622300300964 chr18 78077248 2071467 0.026530994022740145 0.37465447476998964 chr19 59128983 1487342 0.02515419553216398 0.37949005615406844 chr20 63025520 1611919 0.025575655702642357 0.17946422709153415 chr21 48129895 1035050 0.02150534506671997 0.17168762807186688 chr22 51304566 864382 0.016848052081758182 0.13891580549861138 chrMT 16571 30694 1.8522720415183151 1.720354994466321 chrX 155270560 4304904 0.0277251785528435 0.20173046714478327 chrY 59373566 224999 0.003789548365681792 0.12351640734596314