BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524751.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 = 1,270,385
number of mapped reads = 1,136,240 (89.44%)
number of supplementary alignments = 3,671 (0.29%)
number of secondary alignments = 0
number of mapped bases = 65,261,284 bp
number of sequenced bases = 65,240,570 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 31,662
duplication rate = 2.08%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.4143
>>>>>>> ACTG content
number of A's = 16,249,401 bp (24.91%)
number of C's = 12,745,136 bp (19.54%)
number of T's = 20,351,650 bp (31.19%)
number of G's = 15,886,535 bp (24.35%)
number of N's = 7,848 bp (0.01%)
GC percentage = 43.89%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 328,891
number of insertions = 5,456
mapped reads with insertion percentage = 0.48%
number of deletions = 12,781
mapped reads with deletion percentage = 1.12%
homopolymer indels = 40.92%
>>>>>>> Coverage
mean coverageData = 0.0211X
std coverageData = 0.1941X
There is a 1.93% of reference with a coverageData >= 1X
There is a 0.13% 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 5260694 0.021106041697685478 0.23873545417125897
chr2 243199373 5423521 0.02230071950062141 0.2838665593882741
chr3 198022430 4265135 0.02153864589986094 0.15988841705440018
chr4 191154276 4130900 0.021610293457416562 0.1793190345431699
chr5 180915260 3906016 0.021590306975763127 0.1575517256096346
chr6 171115067 3671571 0.021456737062201543 0.1703644708305241
chr7 159138663 3560616 0.02237429882139955 0.23371473689906302
chr8 146364022 3225241 0.022035750015123253 0.17541711822798778
chr9 141213431 2790192 0.01975868711808298 0.17226517846027217
chr10 135534747 3175463 0.023429143229226672 0.24278943249650445
chr11 135006516 2965656 0.021966761959844962 0.1795826303997264
chr12 133851895 2949267 0.022033808337192387 0.16065400086746193
chr13 115169878 2024220 0.01757594985035931 0.1417375165542723
chr14 107349540 1970669 0.018357498318111096 0.14770244409668118
chr15 102531392 1914066 0.018668097278928975 0.14797618352044073
chr16 90354753 2029525 0.022461740335895777 0.17522911323867113
chr17 81195210 1883093 0.02319216860206409 0.1688115758007669
chr18 78077248 1672849 0.02142556305263218 0.24344413471671333
chr19 59128983 1464753 0.024772166299562432 0.2188337860032325
chr20 63025520 1422210 0.022565621037319485 0.1674595973882967
chr21 48129895 878669 0.01825620022649125 0.15998350229963745
chr22 51304566 826872 0.016116928072249945 0.13695716142475267
chrMT 16571 22672 1.3681733148271076 1.3568224179162154
chrX 155270560 3603910 0.0232105171772421 0.17383255478303417
chrY 59373566 223504 0.0037643688101873483 0.11406105499780922