BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237309.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 = 2,085,177 number of mapped reads = 1,834,542 (87.98%) number of supplementary alignments = 16,432 (0.79%) number of secondary alignments = 0 number of mapped bases = 123,615,035 bp number of sequenced bases = 123,561,210 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,086 duplication rate = 5.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4765 >>>>>>> ACTG content number of A's = 34,854,129 bp (28.21%) number of C's = 22,464,495 bp (18.18%) number of T's = 39,772,767 bp (32.19%) number of G's = 26,467,830 bp (21.42%) number of N's = 1,989 bp (0%) GC percentage = 39.6% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 956,594 number of insertions = 9,797 mapped reads with insertion percentage = 0.53% number of deletions = 30,697 mapped reads with deletion percentage = 1.65% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 0.0399X std coverageData = 0.4096X There is a 2.79% of reference with a coverageData >= 1X There is a 0.78% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12002363 0.048153793767278116 0.5689423390812858 chr2 243199373 10147950 0.041726875669206596 0.4456482894392953 chr3 198022430 6755751 0.034116089778314505 0.24787372390891352 chr4 191154276 4121691 0.021562117710618202 0.2225530497178681 chr5 180915260 5738337 0.03171836914144224 0.2387693289702593 chr6 171115067 13753947 0.0803783514867221 0.4710200214869452 chr7 159138663 7013419 0.04407111928544982 0.4928525747348947 chr8 146364022 8845138 0.06043246064938008 0.8684112744523982 chr9 141213431 5820009 0.04121427373292842 0.3912679585453468 chr10 135534747 8483298 0.06259131468331143 0.43788399437068654 chr11 135006516 4038702 0.029914867220186617 0.31349220536641237 chr12 133851895 4794284 0.03581782686005305 0.2602753881079222 chr13 115169878 3742288 0.032493635184713834 0.24302996110254343 chr14 107349540 3563229 0.03319277381160646 0.2626202114509117 chr15 102531392 3371906 0.03288657194861843 0.2460549359022286 chr16 90354753 1813098 0.020066437456809826 0.21025971190716847 chr17 81195210 5282531 0.06505963837029302 0.366515987624766 chr18 78077248 2528232 0.032381161795046874 0.6897815272448156 chr19 59128983 2902073 0.04908038076690749 0.41208475395288524 chr20 63025520 1938982 0.030765029784760204 0.23904798849806483 chr21 48129895 2558214 0.05315228715957099 0.3234680707089501 chr22 51304566 1428193 0.02783754178916551 0.2178380504368551 chrMT 16571 33469 2.0197332689638525 2.247183366597763 chrX 155270560 2667069 0.017176913640293435 0.1946771585125528 chrY 59373566 270862 0.004561996495207985 0.14161038612331622