BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524766.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 = 884,893
number of mapped reads = 816,078 (92.22%)
number of supplementary alignments = 3,793 (0.43%)
number of secondary alignments = 0
number of mapped bases = 47,457,055 bp
number of sequenced bases = 47,441,093 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 20,081
duplication rate = 1.8%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.1852
>>>>>>> ACTG content
number of A's = 12,248,605 bp (25.82%)
number of C's = 9,057,786 bp (19.09%)
number of T's = 15,106,948 bp (31.84%)
number of G's = 11,026,851 bp (23.24%)
number of N's = 903 bp (0%)
GC percentage = 42.34%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 236,217
number of insertions = 3,363
mapped reads with insertion percentage = 0.41%
number of deletions = 10,005
mapped reads with deletion percentage = 1.22%
homopolymer indels = 43.3%
>>>>>>> Coverage
mean coverageData = 0.0153X
std coverageData = 0.1735X
There is a 1.44% of reference with a coverageData >= 1X
There is a 0.06% 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 5152668 0.020672638564860388 0.3101794562368805
chr2 243199373 4041558 0.016618291199295157 0.2141336788867664
chr3 198022430 3854751 0.019466234203872765 0.14619009255251336
chr4 191154276 2792291 0.014607525703479424 0.1307432080404536
chr5 180915260 2182791 0.012065267462788931 0.11461666419883082
chr6 171115067 2437209 0.014243099936956457 0.13439110112313962
chr7 159138663 2827583 0.0177680454686238 0.22855309910696445
chr8 146364022 2259589 0.015438145038129658 0.17218442983359614
chr9 141213431 1568930 0.011110345445823776 0.13059451303238775
chr10 135534747 2609349 0.019252251232667297 0.18326064547268853
chr11 135006516 2215608 0.01641111900110066 0.1532918771221554
chr12 133851895 2171620 0.016224051217205406 0.1343726408217675
chr13 115169878 1528809 0.013274382386686214 0.12080760903239378
chr14 107349540 1829710 0.01704441397699515 0.13806774533051377
chr15 102531392 1328473 0.012956744018456319 0.1204138161790421
chr16 90354753 1262394 0.013971528426401652 0.13029354527962844
chr17 81195210 936063 0.011528549528968519 0.11397581396070877
chr18 78077248 1048946 0.013434720445064868 0.21499846402434533
chr19 59128983 855104 0.014461672713024678 0.21009994955797748
chr20 63025520 861315 0.013666130799079483 0.12325716103509544
chr21 48129895 623904 0.012962920446844939 0.12328874664574063
chr22 51304566 380338 0.007413336271083553 0.08961064750885508
chrMT 16571 56946 3.4364854263472333 2.5734327396502437
chrX 155270560 2488641 0.016027771137039758 0.13814021475908028
chrY 59373566 142465 0.00239946847726815 0.08294620871748193