Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A17 F172 I0 R1	42	33.2	716278	96.8%	693357	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	463,014	C→A	100%	E47* (GAA→TAA)	USA300HOU_0437 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	463,014	0	C	A	99.4%	94.6 / ‑6.7	33	E47* (GAA→TAA)	USA300HOU_0437	hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (13/19); minor base G (1/0); total (14/19)
Fisher's exact test for biased strand distribution p-value = 4.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCCGTCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAATTT  >  CP000730/462877‑463149

gCCGTCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATTTAATAACACATCAATATAACTTCATTCATGTTGTa                                                                                                                                       >  1:246892/1‑140 (MQ=255)

 ccGTCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATaa                                                                                                                                      <  2:229584/140‑1 (MQ=255)

  cGTCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGGGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATaag                                                                                                                                     >  1:237129/1‑140 (MQ=255)

                ttgttgATAATGTCTTTGATTGAATGTATTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGcatcatc                                                                                                                       <  1:157036/140‑1 (MQ=255)

                          tGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTATGTTGTCTTTTGTTGCTTGGTCAGCTTTCTTTTCTATTTATTCTTTTATATTATTTTATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACg                                                                                                             <  1:19954/140‑1 (MQ=255)

                             cTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGt                                                                                                          <  2:179885/140‑1 (MQ=255)

                             cTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGt                                                                                                          <  2:106961/140‑1 (MQ=255)

                                     gaATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTTATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTg                                                                                                  >  2:46523/1‑140 (MQ=255)

                                         gTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGaa                                                                                              >  1:63241/1‑140 (MQ=255)

                                         gTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGaa                                                                                              >  1:130733/1‑140 (MQ=255)

                                                tttATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGACCATTATGAAAATAAACtt                                                                                       >  1:127791/1‑140 (MQ=255)

                                                          aaGTATGATCTTAAGTTGTCTTTTTTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGc                                                                             <  1:105799/140‑1 (MQ=255)

                                                                   cTTAAGTTGGCTTTTGGAGGTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTAcc                                                                    <  2:237129/140‑1 (MQ=255)

                                                                        gTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTCCGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATc                                                               >  2:79126/1‑140 (MQ=255)

                                                                                 tGTAGCTTGGTCGGTATTCTTATCTAATAACTCATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGc                                                      <  1:166972/140‑1 (MQ=255)

                                                                                          gTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTa                                             >  1:329929/1‑140 (MQ=255)

                                                                                            cAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTaaa                                           >  1:136416/1‑140 (MQ=255)

                                                                                            cAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATACTCATGTAGTATGATGCCATTCTGAGAATAAACTTCCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTaaa                                           >  2:127037/1‑140 (MQ=255)

                                                                                                aTTCTTATCTAATAACAAATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGACTAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAacac                                       <  1:106016/140‑1 (MQ=255)

                                                                                                     tATCTAATAACACATCAACATAACTTAATTCATGTTATAAGAAGTTTGCATCATCCTGTCATCCGAGCCCATTTTAAGAATAAACTTTCGCATCTCCTTGATTACCATCTCCAACAACGCCAGTTGCTAAAACACCTTcc                                  <  2:89730/140‑1 (MQ=255)

                                                                                                        cTAATAACACATCAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCAtt                               <  1:116577/140‑1 (MQ=255)

                                                                                                                    cAATATAACTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGctact                   >  1:346143/1‑140 (MQ=255)

                                                                                                                      atatAACTTAATTCATGATATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCCGTTGCTAAAACAACTACCCTTGCCGGTGCTACTaa                 >  1:246596/1‑140 (MQ=255)

                                                                                                                            cTTAATTCTTGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATAGCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCtt           <  1:260473/140‑1 (MQ=255)

                                                                                                                            cTTAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCtt           <  2:31851/140‑1 (MQ=255)

                                                                                                                             ttAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCttt          <  1:335782/140‑1 (MQ=255)

                                                                                                                              tAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCGTATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCtttt         <  1:214977/140‑1 (MQ=255)

                                                                                                                              tAATTCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCtttt         <  1:46523/140‑1 (MQ=255)

                                                                                                                               aaTTCATTTTATGAGAAGTTTGCATCATCATGTAGTTCGAGTCCTTTTTGAGAATCAACTTGCGCATCTGCTGGATTACCATATCCAACAACGCCAGTTGCCATAACACCTGCCATTGCCGTAGCTACTAAAACCtttct        <  2:199336/140‑3 (MQ=255)

                                                                                                                                 ttCATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTaa      <  1:219711/140‑1 (MQ=255)

                                                                                                                                   cATGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAAt    >  1:181741/1‑140 (MQ=255)

                                                                                                                                    aTGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAAtt   <  1:245800/140‑1 (MQ=255)

                                                                                                                                     tGTTATAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACTCCTTCCATTGCTGTAGCTACTGAAACCTTTTTAAAttt  >  1:46423/1‑140 (MQ=255)

GCCGTCTTGTTTAGCTTTGTTGATAATGTCTTTGATTGAATGTAGTCCTTTATCGGCGAAGTATGATCTTAAGTTGTCTTTTGTAGCTTGGTCAGCATTCTTATCTAATAACACATCAATATAACTTAATTCATGTTCTAAGAAGTTTGCATCATCATGTAGTACGAGTCCATTTTGAGAATAAACTTTCGCATCTGCTTGATTACCATATCCAACAACGCCAGTTGCTAAAACACCTACCATTGCCGTAGCTACTAAAACCTTTTTAAATTT  >  CP000730/462877‑463149

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A