BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618642.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 52,759,976 number of mapped reads = 47,213,665 (89.49%) number of supplementary alignments = 288,336 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 25,273,709 number of mapped paired reads (second in pair) = 21,939,956 number of mapped paired reads (both in pair) = 43,264,284 number of mapped paired reads (singletons) = 3,949,381 number of mapped bases = 4,410,139,881 bp number of sequenced bases = 4,406,990,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,848,828 duplication rate = 17.64% >>>>>>> Insert size mean insert size = 171,142.3476 std insert size = 4,098,238.4474 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 53.0526 >>>>>>> ACTG content number of A's = 1,212,186,362 bp (27.51%) number of C's = 949,431,739 bp (21.54%) number of T's = 1,245,288,192 bp (28.26%) number of G's = 999,849,894 bp (22.69%) number of N's = 234,741 bp (0.01%) GC percentage = 44.23% >>>>>>> Mismatches and indels general error rate = 0.0143 number of mismatches = 61,855,013 number of insertions = 841,428 mapped reads with insertion percentage = 1.75% number of deletions = 2,260,829 mapped reads with deletion percentage = 4.67% homopolymer indels = 52.32% >>>>>>> Coverage mean coverageData = 1.4246X std coverageData = 6.1835X There is a 29.72% of reference with a coverageData >= 1X There is a 19.61% of reference with a coverageData >= 2X There is a 14.29% of reference with a coverageData >= 3X There is a 11% of reference with a coverageData >= 4X There is a 8.74% of reference with a coverageData >= 5X There is a 7.11% of reference with a coverageData >= 6X There is a 5.89% of reference with a coverageData >= 7X There is a 4.94% of reference with a coverageData >= 8X There is a 4.2% of reference with a coverageData >= 9X There is a 3.6% of reference with a coverageData >= 10X There is a 3.11% of reference with a coverageData >= 11X There is a 2.7% of reference with a coverageData >= 12X There is a 2.36% of reference with a coverageData >= 13X There is a 2.08% of reference with a coverageData >= 14X There is a 1.83% of reference with a coverageData >= 15X There is a 1.63% of reference with a coverageData >= 16X There is a 1.45% of reference with a coverageData >= 17X There is a 1.3% of reference with a coverageData >= 18X There is a 1.16% of reference with a coverageData >= 19X There is a 1.04% of reference with a coverageData >= 20X There is a 0.94% of reference with a coverageData >= 21X There is a 0.85% of reference with a coverageData >= 22X There is a 0.77% of reference with a coverageData >= 23X There is a 0.7% of reference with a coverageData >= 24X There is a 0.64% of reference with a coverageData >= 25X There is a 0.58% of reference with a coverageData >= 26X There is a 0.53% of reference with a coverageData >= 27X There is a 0.49% of reference with a coverageData >= 28X There is a 0.45% of reference with a coverageData >= 29X There is a 0.41% of reference with a coverageData >= 30X There is a 0.38% of reference with a coverageData >= 31X There is a 0.35% of reference with a coverageData >= 32X There is a 0.32% of reference with a coverageData >= 33X There is a 0.3% of reference with a coverageData >= 34X There is a 0.28% of reference with a coverageData >= 35X There is a 0.26% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 369519018 1.4825199492682508 6.534226034003532 chr2 243199373 380089009 1.5628700202282182 8.154495118185237 chr3 198022430 293912684 1.4842393561173852 5.085486189361854 chr4 191154276 232014921 1.213757420733816 4.957642277541107 chr5 180915260 257316765 1.4223054760554747 5.3646981258948445 chr6 171115067 245967138 1.4374370551483933 4.846227909472549 chr7 159138663 214902309 1.350409164867748 4.931340513804016 chr8 146364022 219196638 1.497612835482206 5.187161019775452 chr9 141213431 188214372 1.3328361945968157 6.213269120539653 chr10 135534747 222631091 1.642612657844855 5.675947551348753 chr11 135006516 223820276 1.6578479515759077 6.706410318634073 chr12 133851895 189753385 1.4176368963622068 5.171754453415235 chr13 115169878 119174957 1.0347754036867174 4.215492362082928 chr14 107349540 135892050 1.2658838593998634 4.81389326767926 chr15 102531392 143962155 1.4040788112971294 5.3793106655590455 chr16 90354753 151066658 1.6719281829036707 13.720877554760522 chr17 81195210 138164164 1.7016294926757378 5.872306781184443 chr18 78077248 113166580 1.4494181454756192 6.029574428661812 chr19 59128983 89106360 1.5069827938694633 7.023963547500033 chr20 63025520 120036248 1.9045657695485891 6.11215063571784 chr21 48129895 56513174 1.1741802885711676 7.480702956232179 chr22 51304566 69433756 1.3533640651009502 5.831352470023736 chrMT 16571 35640 2.150745277895118 7.128113114450989 chrX 155270560 227546618 1.4654846224551519 4.706187674346932 chrY 59373566 8703915 0.1465957931514506 5.429606280634437