BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524976.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 = 1,795,044
number of mapped reads = 1,631,740 (90.9%)
number of supplementary alignments = 3,736 (0.21%)
number of secondary alignments = 0
number of mapped bases = 95,293,241 bp
number of sequenced bases = 95,262,990 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 62,591
duplication rate = 2.9%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7497
>>>>>>> ACTG content
number of A's = 24,539,324 bp (25.76%)
number of C's = 17,623,740 bp (18.5%)
number of T's = 30,545,530 bp (32.06%)
number of G's = 22,553,423 bp (23.67%)
number of N's = 973 bp (0%)
GC percentage = 42.17%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 462,897
number of insertions = 6,214
mapped reads with insertion percentage = 0.38%
number of deletions = 17,655
mapped reads with deletion percentage = 1.07%
homopolymer indels = 42.13%
>>>>>>> Coverage
mean coverageData = 0.0308X
std coverageData = 0.2651X
There is a 2.75% of reference with a coverageData >= 1X
There is a 0.24% of reference with a coverageData >= 2X
There is a 0.03% 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 7612072 0.030539831633960103 0.4464084924970728
chr2 243199373 8066689 0.033169036994186656 0.3040262294868551
chr3 198022430 6389562 0.03226685987036923 0.19697478585829936
chr4 191154276 6190599 0.03238535453949249 0.22278673479195402
chr5 180915260 5726840 0.03165482005221671 0.19657163580609588
chr6 171115067 5524938 0.03228785224389387 0.23438599911228758
chr7 159138663 5247294 0.03297309340848239 0.3190628391051799
chr8 146364022 4862814 0.03322410749275529 0.27670025662865805
chr9 141213431 3975417 0.028151833517875507 0.2434244065092145
chr10 135534747 4611747 0.034026307659688185 0.28983590372995444
chr11 135006516 4280883 0.0317087139705168 0.26342515464348676
chr12 133851895 4332008 0.032364188792396255 0.19866927593760908
chr13 115169878 2976227 0.0258420608902616 0.17653555937256168
chr14 107349540 2917924 0.02718152308803559 0.18536344315053854
chr15 102531392 2732500 0.02665037455065469 0.19156644433497702
chr16 90354753 2743052 0.030358690704406 0.20201521647205842
chr17 81195210 2559025 0.03151694539616315 0.21761754369562417
chr18 78077248 2594943 0.033235584840285354 0.36774864559476683
chr19 59128983 1858427 0.0314300518241621 0.3263603147329083
chr20 63025520 2023083 0.032099425756423744 0.20212140987754842
chr21 48129895 1261649 0.02621341683791332 0.19676095493527854
chr22 51304566 1106444 0.021566189644796917 0.16042301338871792
chrMT 16571 375 0.022629895600748295 0.14872048757937667
chrX 155270560 5410471 0.03484544011433977 0.2236113357079414
chrY 59373566 288258 0.004854988834593496 0.13350551382568068