BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525055.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 = 1,152,096
number of mapped reads = 1,058,493 (91.88%)
number of supplementary alignments = 4,708 (0.41%)
number of secondary alignments = 0
number of mapped bases = 61,196,289 bp
number of sequenced bases = 61,179,831 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 23,799
duplication rate = 1.69%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.8006
>>>>>>> ACTG content
number of A's = 15,106,174 bp (24.69%)
number of C's = 11,038,530 bp (18.04%)
number of T's = 19,904,902 bp (32.54%)
number of G's = 15,128,336 bp (24.73%)
number of N's = 1,889 bp (0%)
GC percentage = 42.77%
>>>>>>> Mismatches and indels
general error rate = 0.0048
number of mismatches = 287,432
number of insertions = 3,206
mapped reads with insertion percentage = 0.3%
number of deletions = 9,667
mapped reads with deletion percentage = 0.91%
homopolymer indels = 44.89%
>>>>>>> Coverage
mean coverageData = 0.0198X
std coverageData = 0.1856X
There is a 1.83% of reference with a coverageData >= 1X
There is a 0.11% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% 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 4878461 0.019572512920639825 0.29628934439068666
chr2 243199373 5203365 0.021395470456249902 0.19739996533704743
chr3 198022430 4308499 0.021757631193597613 0.15603731438917606
chr4 191154276 4055219 0.02121437764750813 0.16615692907083873
chr5 180915260 3748881 0.020721751166816994 0.15280678859987362
chr6 171115067 3459048 0.020214748243063834 0.15978810772180227
chr7 159138663 3423622 0.02151345207669616 0.20257166328659695
chr8 146364022 3169611 0.021655670271209137 0.19676394222424493
chr9 141213431 2483598 0.01758754802862909 0.17737975164812694
chr10 135534747 2974571 0.021946925536371866 0.19828956784448867
chr11 135006516 2834369 0.020994312600437746 0.18014144523587644
chr12 133851895 2781894 0.02078337404188413 0.1548878994253109
chr13 115169878 1943510 0.016875158971688762 0.13688185505199665
chr14 107349540 1879408 0.017507368918394994 0.14533985690628773
chr15 102531392 1617927 0.015779820876712567 0.13294414548213526
chr16 90354753 1748463 0.019351090473347873 0.15234024623935527
chr17 81195210 1524348 0.018773866093824993 0.1499615364382216
chr18 78077248 1701607 0.02179389058384845 0.2709794616687244
chr19 59128983 1071526 0.018121840519394694 0.22531882412866888
chr20 63025520 1247848 0.019799090907936974 0.15346683609268438
chr21 48129895 788865 0.01639033286899961 0.1445945319691668
chr22 51304566 634497 0.012367261814474758 0.11735119098568006
chrMT 16571 4185 0.25254963490435095 0.5193489235561733
chrX 155270560 3537244 0.022781163409212924 0.17044714524835194
chrY 59373566 175723 0.0029596167425753068 0.08203271397022988