BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716986.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 = 1,913,888 number of mapped reads = 1,759,774 (91.95%) number of supplementary alignments = 10,920 (0.57%) number of secondary alignments = 0 number of mapped bases = 102,777,545 bp number of sequenced bases = 102,747,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,778 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4438 >>>>>>> ACTG content number of A's = 26,484,699 bp (25.78%) number of C's = 20,896,526 bp (20.34%) number of T's = 31,299,676 bp (30.46%) number of G's = 24,065,463 bp (23.42%) number of N's = 1,207 bp (0%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 513,610 number of insertions = 6,588 mapped reads with insertion percentage = 0.37% number of deletions = 19,124 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.43% >>>>>>> Coverage mean coverageData = 0.0332X std coverageData = 0.3148X There is a 2.94% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8302996 0.03331183676368855 0.41369327591345567 chr2 243199373 9849698 0.040500507375896895 0.3735192146247773 chr3 198022430 7630471 0.03853336715441781 0.2304203926990849 chr4 191154276 5529419 0.02892647298143621 0.2087555765224997 chr5 180915260 5097407 0.028175660803848167 0.1853584792419467 chr6 171115067 5560776 0.032497290259074614 0.21628959637258358 chr7 159138663 6266982 0.0393806375010201 0.7052567791217116 chr8 146364022 8363942 0.05714479477750345 0.3509344160780229 chr9 141213431 4226038 0.029926600961915583 0.2205285442934316 chr10 135534747 4736588 0.03494740725048168 0.4126144746793575 chr11 135006516 3694966 0.027368797517891653 0.2181200546455746 chr12 133851895 4709691 0.03518583730174309 0.22910891351146967 chr13 115169878 2552663 0.022164328419276437 0.1622614665438719 chr14 107349540 3230649 0.03009467017744091 0.19629631344082257 chr15 102531392 2374573 0.023159472954390397 0.17131314289354047 chr16 90354753 3092141 0.03422222846428455 0.21332506274477472 chr17 81195210 4317903 0.05317928237392329 0.26453430081794393 chr18 78077248 2325799 0.029788434653844356 0.3425804381574116 chr19 59128983 2082313 0.03521645214158343 0.37771669276551206 chr20 63025520 2265068 0.035938902209771535 0.22000714756572942 chr21 48129895 1036690 0.021539419522938915 0.1698631156302498 chr22 51304566 1543388 0.030082858512047447 0.18993615529036473 chrMT 16571 273560 16.50835797477521 10.210216805952866 chrX 155270560 3486535 0.022454578640020362 0.18942627493728587 chrY 59373566 227289 0.0038281177182451867 0.10663600662944928