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
A23 F58 I0 R1	19	25.6	590480	94.5%	558003	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,450	A→T	27.6%	F74L (TTT→TTA)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,450	0	A	T	27.6%	31.4 / 13.6	26	F74L (TTT→TTA)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base A (7/11); new base T (4/3); total (11/15)
Fisher's exact test for biased strand distribution p-value = 6.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.50e-01

TCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTAT  >  USA300TCH1516_ALE/1744316‑1744589

tcatcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCa                                                                                                                                       <  1:133523/141‑1 (MQ=255)

  atcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGTTGCAAAGCCAAt                                                                                                                                     >  1:251883/1‑141 (MQ=255)

    cTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTAACATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTCCTCTTCTAACAGGTGCAAAGCCAATcc                                                                                                                                   >  2:290849/1‑141 (MQ=255)

          ttAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACTTTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATTCCCATTg                                                                                                                             >  1:163789/1‑141 (MQ=255)

            aaCACTCGTTTACCTAGTTTAATTGCATCTTTGTGCATTGGTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGaa                                                                                                                           <  1:277240/141‑1 (MQ=255)

                cacGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATGCCCATTGAATAAg                                                                                                                       >  2:140767/1‑141 (MQ=255)

                       aCCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAgg                                                                                                                >  1:87573/1‑141 (MQ=255)

                                    gCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACGCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATa                                                                                                   <  2:237935/141‑1 (MQ=255)

                                                aTTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACTCGCt                                                                                       >  2:197653/1‑141 (MQ=255)

                                                          aagttGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTa                                                                             <  2:86019/138‑1 (MQ=255)

                                                           aTTTGTACCATATTCTAGGTCATACTCATAACGAATCACTTCCAGAGGGAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTAc                                                                            <  1:55128/141‑1 (MQ=255)

                                                               gTACCATATTCTAGGTCATACTCATAACGAATGACTTCCCTGGCTAATTTCCCTTCTGTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACg                                                                        <  2:221622/141‑1 (MQ=255)

                                                                           aGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACAtct                                                            >  1:176572/1‑141 (MQ=255)

                                                                              tCACACTCATAACTAATGACTTCCCGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTg                                                         <  1:79306/141‑1 (MQ=255)

                                                                                      aTAACGAATGACTTCACGAGGTAATTTCCCAACGTTTCTATCTCAGACGTGTGCTATTCCGATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGc                                                 <  1:290849/141‑1 (MQ=255)

                                                                                           gAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAGCATCTCTGTCTTTTGCTTAtt                                            >  1:122565/1‑141 (MQ=255)

                                                                                                 cTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACaa                                      >  1:161959/1‑141 (MQ=255)

                                                                                                    cACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAAttt                                   <  2:87573/141‑1 (MQ=255)

                                                                                                                        tttCTAACAGGTGCTAAGCCACTCCCCATTGAATCAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCatat               <  1:226400/141‑1 (MQ=255)

                                                                                                                         ttttAACAGGTGGTAAGTTAATTTCTATTTAATAAGTTATAGGACAGTTAATGATAAAGCCACGCGCTTCAGGTCCTAAAACGATATCAAAATCTTTGTCTTTTGCGTATTCTACAATTTTATCTGTTTCATAGCCATATg              <  2:23029/138‑1 (MQ=255)

                                                                                                                         ttCTAACAGTTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATg              <  1:247600/141‑1 (MQ=255)

                                                                                                                         ttCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATg              <  1:133550/141‑1 (MQ=255)

                                                                                                                          tCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTATAATTTTATCTGTTGCATAGCCATATgg             >  1:174357/1‑140 (MQ=255)

                                                                                                                           cTAACAGGTGCTAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCt            >  2:171254/1‑141 (MQ=255)

                                                                                                                                    gCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTa   <  1:78084/141‑1 (MQ=255)

                                                                                                                                     cAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTAt  <  1:188813/141‑1 (MQ=255)

TCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTAT  >  USA300TCH1516_ALE/1744316‑1744589

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