BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716180.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 = 1,198,523
number of mapped reads = 1,024,212 (85.46%)
number of supplementary alignments = 3,954 (0.33%)
number of secondary alignments = 0
number of mapped bases = 59,676,898 bp
number of sequenced bases = 59,659,392 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 24,823
duplication rate = 1.84%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.7327
>>>>>>> ACTG content
number of A's = 16,040,096 bp (26.89%)
number of C's = 11,180,058 bp (18.74%)
number of T's = 18,237,861 bp (30.57%)
number of G's = 14,200,914 bp (23.8%)
number of N's = 463 bp (0%)
GC percentage = 42.54%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 301,903
number of insertions = 4,895
mapped reads with insertion percentage = 0.48%
number of deletions = 10,967
mapped reads with deletion percentage = 1.06%
homopolymer indels = 40.3%
>>>>>>> Coverage
mean coverageData = 0.0193X
std coverageData = 0.1796X
There is a 1.77% of reference with a coverageData >= 1X
There is a 0.12% 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 4763435 0.01911102560502748 0.22249732015549883
chr2 243199373 4942219 0.020321676569453984 0.23240373366375497
chr3 198022430 4022613 0.020313926053730377 0.15269996864619373
chr4 191154276 3792958 0.019842391597873543 0.16321725007271437
chr5 180915260 3616585 0.019990491681022377 0.15106135220155886
chr6 171115067 3422135 0.01999902790559057 0.16178865718432875
chr7 159138663 3283496 0.020632924382429932 0.21526723300413772
chr8 146364022 3043709 0.020795472537643165 0.19301603713200768
chr9 141213431 2529422 0.01791204973980131 0.1616443558939408
chr10 135534747 2868499 0.02116430703928639 0.21429248873581988
chr11 135006516 2667412 0.01975765377131871 0.17151645771702667
chr12 133851895 2740501 0.02047412926055324 0.15462150759141524
chr13 115169878 1872708 0.016260397532069974 0.13721383861526132
chr14 107349540 1811722 0.016876849216121467 0.14435363905194074
chr15 102531392 1716280 0.016739068557656958 0.1403085350015239
chr16 90354753 1751144 0.019380762404386187 0.15721298411170045
chr17 81195210 1678731 0.020675246729456084 0.1578855641065309
chr18 78077248 1553690 0.01989939501966053 0.24384076625823564
chr19 59128983 1270922 0.021494061550153837 0.21014102932228412
chr20 63025520 1288214 0.020439561625195637 0.1553157426781447
chr21 48129895 783574 0.016280401193478605 0.1450831128457676
chr22 51304566 744801 0.01451724589191535 0.1297945755294215
chrMT 16571 2032 0.12262386096192143 0.4290762985872983
chrX 155270560 3317568 0.02136636848608004 0.16280821915363097
chrY 59373566 192528 0.003242655157347295 0.10317811437589151