BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525004.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 = 1,528,639
number of mapped reads = 1,378,057 (90.15%)
number of supplementary alignments = 5,010 (0.33%)
number of secondary alignments = 0
number of mapped bases = 78,565,916 bp
number of sequenced bases = 78,541,205 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 36,117
duplication rate = 1.78%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.4394
>>>>>>> ACTG content
number of A's = 19,626,767 bp (24.99%)
number of C's = 14,537,760 bp (18.51%)
number of T's = 25,288,940 bp (32.2%)
number of G's = 19,086,863 bp (24.3%)
number of N's = 875 bp (0%)
GC percentage = 42.81%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 393,398
number of insertions = 5,289
mapped reads with insertion percentage = 0.38%
number of deletions = 14,988
mapped reads with deletion percentage = 1.08%
homopolymer indels = 42.7%
>>>>>>> Coverage
mean coverageData = 0.0254X
std coverageData = 0.2401X
There is a 2.34% of reference with a coverageData >= 1X
There is a 0.14% of reference with a coverageData >= 2X
There is a 0.02% 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 8415441 0.03376296903990462 0.449264447798429
chr2 243199373 7479662 0.03075526843566328 0.2728424830240902
chr3 198022430 4339013 0.021911724848543673 0.1592895968015935
chr4 191154276 5058776 0.026464362220178637 0.18176989227265022
chr5 180915260 3420940 0.018909073784046743 0.14942089967136757
chr6 171115067 5265788 0.030773374269841475 0.24967458030509393
chr7 159138663 4981116 0.03130047661642099 0.33528256373597815
chr8 146364022 4788303 0.03271502746761086 0.23045050318368765
chr9 141213431 2174399 0.01539796168538671 0.17370055060017422
chr10 135534747 3983822 0.029393362869523047 0.24123334206201955
chr11 135006516 3329268 0.024660054185829075 0.21928943630157455
chr12 133851895 4311140 0.032208285134849975 0.19226563703026694
chr13 115169878 1522390 0.013218647327211721 0.12337572700403175
chr14 107349540 1798752 0.016756028949914455 0.14175096883404628
chr15 102531392 2189750 0.021356873805048898 0.167119167204172
chr16 90354753 2543562 0.028150837842476312 0.18740626270180882
chr17 81195210 2084003 0.02566657565144545 0.22403348187936226
chr18 78077248 1507040 0.01930190982141174 0.2651714327686406
chr19 59128983 1952034 0.03301315025154415 0.29031658845329683
chr20 63025520 1889191 0.029975016469519014 0.1853888047433475
chr21 48129895 902023 0.01874142879389203 0.15029735864146015
chr22 51304566 1058326 0.020628300412871635 0.15188025720107465
chrMT 16571 19248 1.1615472813952086 1.1865553928502603
chrX 155270560 3346534 0.021552920270268876 0.18294518098026039
chrY 59373566 205395 0.0034593677597198726 0.08452113647006819