BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716529.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 = 1,347,880
number of mapped reads = 1,264,073 (93.78%)
number of supplementary alignments = 26,478 (1.96%)
number of secondary alignments = 0
number of mapped bases = 100,121,976 bp
number of sequenced bases = 100,076,509 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 40,265
duplication rate = 2.21%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.2826
>>>>>>> ACTG content
number of A's = 25,742,963 bp (25.72%)
number of C's = 19,603,594 bp (19.59%)
number of T's = 30,883,977 bp (30.86%)
number of G's = 23,839,332 bp (23.82%)
number of N's = 6,643 bp (0.01%)
GC percentage = 43.41%
>>>>>>> Mismatches and indels
general error rate = 0.0066
number of mismatches = 642,715
number of insertions = 8,386
mapped reads with insertion percentage = 0.65%
number of deletions = 23,879
mapped reads with deletion percentage = 1.86%
homopolymer indels = 42.07%
>>>>>>> Coverage
mean coverageData = 0.0323X
std coverageData = 0.3194X
There is a 2.86% of reference with a coverageData >= 1X
There is a 0.26% 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 9768851 0.03919288530077524 0.6494137562898282
chr2 243199373 8291472 0.03409331158102945 0.34177032092916365
chr3 198022430 6416415 0.03240246572067619 0.1957753651009513
chr4 191154276 6325070 0.033088822977729256 0.23502656645230952
chr5 180915260 5854891 0.032362615514025736 0.19767934845641022
chr6 171115067 5557538 0.032478367319927474 0.2114170086644738
chr7 159138663 5178367 0.032539967990054056 0.37518771021026814
chr8 146364022 4854251 0.03316560267795866 0.35364278086221806
chr9 141213431 4072597 0.02884001168415772 0.26553696933795934
chr10 135534747 4606038 0.03398418561994291 0.31618409861407637
chr11 135006516 5596183 0.04145120669583089 0.35419265612757955
chr12 133851895 4375843 0.03269167761875915 0.19853701506858343
chr13 115169878 3533620 0.030681807269084718 0.1922586442313714
chr14 107349540 2912408 0.02713013954228402 0.1939427587688647
chr15 102531392 2748762 0.026808979634256793 0.17782558517951796
chr16 90354753 2280466 0.025239026440590236 0.19009991635290857
chr17 81195210 3010048 0.03707174351787501 0.2419032484890253
chr18 78077248 2586065 0.03312187693910523 0.43796841936886793
chr19 59128983 1872140 0.03166196854764101 0.44833268356447475
chr20 63025520 2063615 0.03274253032739754 0.20576930601149457
chr21 48129895 1309030 0.027197856966029117 0.20161112035311024
chr22 51304566 1094290 0.02132929065221992 0.158953346295886
chrMT 16571 57379 3.4626154124675637 2.7649551910844505
chrX 155270560 5459169 0.03515907329760387 0.23722370403460388
chrY 59373566 297468 0.0050101083704488965 0.1615084027202553