BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3081938.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,508,881
number of mapped reads = 2,287,361 (91.17%)
number of supplementary alignments = 14,111 (0.56%)
number of secondary alignments = 0
number of mapped bases = 154,533,544 bp
number of sequenced bases = 154,479,072 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 119,914
duplication rate = 3.92%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.0194
>>>>>>> ACTG content
number of A's = 43,252,656 bp (28%)
number of C's = 28,298,333 bp (18.32%)
number of T's = 49,105,039 bp (31.79%)
number of G's = 33,803,722 bp (21.88%)
number of N's = 19,322 bp (0.01%)
GC percentage = 40.2%
>>>>>>> Mismatches and indels
general error rate = 0.0078
number of mismatches = 1,183,425
number of insertions = 10,801
mapped reads with insertion percentage = 0.47%
number of deletions = 30,896
mapped reads with deletion percentage = 1.34%
homopolymer indels = 48.02%
>>>>>>> Coverage
mean coverageData = 0.0499X
std coverageData = 0.491X
There is a 4.3% of reference with a coverageData >= 1X
There is a 0.49% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 13917629 0.055837890971593605 0.8434967999758237
chr2 243199373 13220811 0.05436202748762843 0.7065015833798173
chr3 198022430 9763186 0.0493034349694628 0.2508702955099238
chr4 191154276 7780240 0.04070136521560208 0.25083551118331265
chr5 180915260 8807413 0.04868253236349438 0.2502108526236558
chr6 171115067 13462418 0.07867464996521902 0.4390789559117576
chr7 159138663 9903909 0.06223446152742907 0.6917055001540782
chr8 146364022 8756406 0.059826218768434775 0.6037662515426442
chr9 141213431 8952058 0.06339381414789079 0.5565604684207311
chr10 135534747 6190434 0.04567414730925052 0.48793867302968197
chr11 135006516 6856412 0.05078578577644356 0.36389958352332086
chr12 133851895 6461503 0.04827352649732751 0.26855729899750996
chr13 115169878 4132571 0.035882394526805 0.21073940973398197
chr14 107349540 3810677 0.035497841909709164 0.255155132573608
chr15 102531392 3370842 0.032876194639003826 0.20492412599407261
chr16 90354753 3273368 0.036227955822091616 0.26891869947182606
chr17 81195210 4741606 0.05839760744506973 0.3234564360441625
chr18 78077248 4693906 0.06011874291470929 0.8582740735608814
chr19 59128983 2139092 0.03617670880623805 0.7103577348029563
chr20 63025520 3790358 0.060140051204654876 0.28509238639455486
chr21 48129895 1579867 0.032825066416621106 0.2470298773299893
chr22 51304566 1121571 0.021861036696032083 0.1614977312683513
chrMT 16571 12679 0.765131856858367 1.030549995859774
chrX 155270560 7451560 0.04799081036353575 0.3149490089052181
chrY 59373566 343028 0.005777453218828056 0.1609012899251902