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
A1 F56 I0 R1	19	43.9	998620	94.5%	943695	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,607	T→C	100%	D22G (GAT→GGT)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,607	0	T	C	88.2%	69.8 / 2.1	33	D22G (GAT→GGT)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base T (4/0); new base C (16/10); total (22/11)
Fisher's exact test for biased strand distribution p-value = 2.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGATA  >  USA300TCH1516_ALE/1744471‑1744743

aGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCtt                                                                                                                                      <  1:441695/141‑1 (MQ=255)

    aCAGGACAGCCAATGATAAAGCCACGCGCATCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATACTTCTAGTAATAACCTTGcaa                                                                                                                                  >  2:283625/1‑141 (MQ=255)

     cAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAAc                                                                                                                                 <  2:244467/141‑1 (MQ=255)

              cAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTg                                                                                                                        >  1:323226/1‑141 (MQ=255)

              cAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATAACAACATCTCTGTCTTTTGCGTCTTCTACAATTTTATCAGTTTCATCGCCATCAGCTTCAACACAATCACTAATTGTCGTAATAAACTTCTAACTAccacgtc                                                                                                                        >  2:128067/1‑138 (MQ=255)

                 tGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCACCATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGtt                                                                                                                     >  1:416334/1‑141 (MQ=255)

                     aaaGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATACTTCTAGTAATACCCTTGACTCTAACATATGGttgatt                                                                                                                 >  1:231009/1‑137 (MQ=255)

                              cgcTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCTTTGAAACTAACACCTGGTTTCGGCCAATCTTg                                                                                                        >  1:246851/1‑141 (MQ=255)

                              cgcTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTg                                                                                                        <  1:41125/141‑1 (MQ=255)

                                 ttCAGGTCCTACAACGATATCAACATCTCTGTCATTTGCGTATTCTACAATTTTATCTGTTGCCTAGCAATATGCTTCACCATTATACATAATTGTAGTAATATCCTTGAAACTAACAACTGGTTTCCGCCAATCTTCAAc                                                                                                     >  2:204873/1‑141 (MQ=255)

                                  tCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACt                                                                                                    <  1:421705/141‑1 (MQ=255)

                                    gggTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATACTCGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTc                                                                                                  <  2:486122/140‑1 (MQ=255)

                                             aaCGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTa                                                                                         <  1:27611/141‑1 (MQ=255)

                                                  tatCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCt                                                                                    >  1:12727/1‑141 (MQ=255)

                                                   atCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTCTTGCtt                                                                                   >  2:217927/1‑141 (MQ=255)

                                                    tCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCttt                                                                                  >  1:166370/1‑141 (MQ=255)

                                                      aaCATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTaa                                                                                >  2:262886/1‑141 (MQ=255)

                                                       ccctctcTTTCATTGGCGTATGTTACCATTTGAGCCGTTGAACAGCCATATTCTTCACTATTATCCATAATTGTAGTAATAACCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACTTAGTGCTTTaaa                                                                               <  2:260404/138‑1 (MQ=255)

                                                                 cTTTTGCTTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACTCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAata                                                                     <  1:38562/141‑1 (MQ=255)

                                                                 cTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAata                                                                     >  1:155796/1‑141 (MQ=255)

                                                                                       aTCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAACCTAACCCCTGGTTTCGGCCAATCTTGAACTTCTGATCCGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTcccca                                               >  2:405201/1‑137 (MQ=255)

                                                                                       aTCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTCATATTTCCTCCTAAATTGCGCACGa                                               >  1:184627/1‑141 (MQ=255)

                                                                                       aTCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGa                                               <  1:197194/141‑1 (MQ=255)

                                                                                          tGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGCACTTTGGAGACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACaa                                            >  1:18598/1‑141 (MQ=255)

                                                                                              gCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATtgt                                        <  1:332740/141‑1 (MQ=255)

                                                                                                aTAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGCATTGCTTTCAATCCATTAATATTTCCTCCTCAATTGCTCACTACAAttatca                                      >  1:481061/1‑137 (MQ=255)

                                                                                                aTAGCCATATGCTTCACCATTATCCATAATTGTAGTAATACCCTTGAAACTAAAAACTTTGGTCGGGCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGa                                      >  1:71633/1‑141 (MQ=255)

                                                                                                        atGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATcc                              >  1:185090/1‑141 (MQ=255)

                                                                                                                        cATAATTGTAGTAATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGa              <  1:247839/141‑1 (MQ=255)

                                                                                                                               gtagtaATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCACTTTTTTATTTCTGAAGActct       >  2:184099/1‑141 (MQ=255)

                                                                                                                               gtagtaATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCt       >  1:259910/1‑141 (MQ=255)

                                                                                                                                 agtaATACCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATACAATTTTTTATTTCTGAAAAATCttt     >  2:324777/1‑140 (MQ=255)

                                                                                                                                    aaTATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTTTGAAATCTTGata  >  1:311535/1‑141 (MQ=255)

AGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTCACCATTATCCATAATTGTAGTAATATCCTTGAAACTAACACCTGGTTTCGGCCAATCTTGAACTTCTGATACGTATTGCTTTAAATCCATTAATATTTCCTCCTAAATTGCTCACGACAATTGTGACTTTATCCAATTTTTTATTTCTGAAAAATCTTGATA  >  USA300TCH1516_ALE/1744471‑1744743

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