BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR927058.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 28,828,920
number of mapped reads = 28,459,657 (98.72%)
number of supplementary alignments = 223,268 (0.77%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 14,274,365
number of mapped paired reads (second in pair) = 14,185,292
number of mapped paired reads (both in pair) = 28,271,082
number of mapped paired reads (singletons) = 188,575
number of mapped bases = 2,743,495,348 bp
number of sequenced bases = 2,741,350,690 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,736,086
duplication rate = 4.78%
>>>>>>> Insert size
mean insert size = 80,099.5193
std insert size = 2,763,721.1382
median insert size = 186
>>>>>>> Mapping quality
mean mapping quality = 53.752
>>>>>>> ACTG content
number of A's = 805,143,656 bp (29.37%)
number of C's = 540,762,856 bp (19.73%)
number of T's = 811,273,384 bp (29.59%)
number of G's = 583,922,045 bp (21.3%)
number of N's = 248,749 bp (0.01%)
GC percentage = 41.03%
>>>>>>> Mismatches and indels
general error rate = 0.0095
number of mismatches = 25,279,216
number of insertions = 463,222
mapped reads with insertion percentage = 1.6%
number of deletions = 1,521,539
mapped reads with deletion percentage = 5.2%
homopolymer indels = 53.48%
>>>>>>> Coverage
mean coverageData = 0.8862X
std coverageData = 3.4044X
There is a 32.44% of reference with a coverageData >= 1X
There is a 19.21% of reference with a coverageData >= 2X
There is a 11.67% of reference with a coverageData >= 3X
There is a 7.5% of reference with a coverageData >= 4X
There is a 4.95% of reference with a coverageData >= 5X
There is a 3.35% of reference with a coverageData >= 6X
There is a 2.31% of reference with a coverageData >= 7X
There is a 1.61% of reference with a coverageData >= 8X
There is a 1.14% of reference with a coverageData >= 9X
There is a 0.82% of reference with a coverageData >= 10X
There is a 0.59% of reference with a coverageData >= 11X
There is a 0.43% of reference with a coverageData >= 12X
There is a 0.32% of reference with a coverageData >= 13X
There is a 0.24% of reference with a coverageData >= 14X
There is a 0.18% of reference with a coverageData >= 15X
There is a 0.14% of reference with a coverageData >= 16X
There is a 0.1% of reference with a coverageData >= 17X
There is a 0.08% of reference with a coverageData >= 18X
There is a 0.06% of reference with a coverageData >= 19X
There is a 0.05% of reference with a coverageData >= 20X
There is a 0.04% of reference with a coverageData >= 21X
There is a 0.03% of reference with a coverageData >= 22X
There is a 0.03% of reference with a coverageData >= 23X
There is a 0.02% of reference with a coverageData >= 24X
There is a 0.02% of reference with a coverageData >= 25X
There is a 0.02% of reference with a coverageData >= 26X
There is a 0.02% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 212550655 0.8527587780814395 4.252849454394391
chr2 243199373 238243486 0.9796221226277586 5.716483839366401
chr3 198022430 184287817 0.9306411248463116 1.9463948638229458
chr4 191154276 162691594 0.8511009923733016 2.7995528232980473
chr5 180915260 170684734 0.9434512821085408 1.9341780120137817
chr6 171115067 162193086 0.947859758018854 2.0482513427262763
chr7 159138663 149720732 0.9408193406777585 2.8066815391502127
chr8 146364022 138143046 0.9438319889842874 2.28044843647322
chr9 141213431 113082579 0.8007919515814328 4.06067025025324
chr10 135534747 134297013 0.9908677735606796 6.444820814352328
chr11 135006516 136528054 1.0112701078813116 3.49231677188179
chr12 133851895 126623340 0.9459958710334284 2.2528312719967674
chr13 115169878 87959033 0.7637329701781919 1.8352394395608456
chr14 107349540 82112393 0.7649067988554027 1.80900602126962
chr15 102531392 80636902 0.7864606188122365 1.9053218541756338
chr16 90354753 86535213 0.9577272929958649 4.851950111332507
chr17 81195210 68524897 0.843952457293971 2.626996401707171
chr18 78077248 79908230 1.0234509033924966 4.2827948950727155
chr19 59128983 37515941 0.6344763447056074 2.48972931074988
chr20 63025520 65389764 1.0375124870052639 2.2692613960279417
chr21 48129895 36121061 0.7504911656258548 2.250345968319007
chr22 51304566 29852889 0.5818758704634593 1.6717886935447805
chrMT 16571 19370 1.1689095407639853 1.581814703307684
chrX 155270560 155910517 1.0041215604555043 2.332574814756141
chrY 59373566 3963002 0.0667469088853447 2.0884357460092065