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 F169 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,482,693	T→C	23.0%	A329A (GCT→GCC)	hssS →	Heme sensor protein HssS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,482,693	0	T	C	23.0%	70.4 / 18.0	39	A329A (GCT→GCC)	hssS	Heme sensor protein HssS
Reads supporting (aligned to +/- strand): ref base T (13/17); new base C (5/4); total (18/21)
Fisher's exact test for biased strand distribution p-value = 7.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01

TTACAACGCAGCTGAGCGGATTAACAACTGAATTGTTGCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATTTATTAATAAATGCTATTAAGTATACAGATGTTGGTGGTGCC  >  USA300TCH1516_ALE/2482557‑2482825

ttACAACGCAGCTGAGCGGATTAACAACTGAATTGTTGCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGctgctg                                                                                                                                  >  2:253895/1‑141 (MQ=255)

ttACAACGCAGCTGAGCGGATTAACAACTGAATTGTTGCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGctgctg                                                                                                                                  >  2:207072/1‑141 (MQ=255)

    aaCGCAGTTGAGCGGATTAACAACTTAATTGTTGCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCATGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCtgatga                                                                                                                              <  1:265564/141‑1 (MQ=255)

    aaCGCAGCTGAGCGGATTAACAACTGAATTGTTGCTCTTATCCGAATTAGAGAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCCGCtgatga                                                                                                                              >  2:77893/1‑141 (MQ=255)

      cGCAGCTGAGCGGATTAACAACTGAATTGTTGCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGaaa                                                                                                                            >  1:358081/1‑141 (MQ=255)

        cAGCTGAGCGGATTAACAACTGAATTGTTGCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAg                                                                                                                          <  2:352113/141‑1 (MQ=255)

         agcggagcggATTAACAACTGAATTGTTGCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGt                                                                                                                         <  1:93379/141‑1 (MQ=255)

            tGAGCGGATTAACAACTGAATTGTTGCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCCGCTGATGAAAAGTCGt                                                                                                                      >  2:229927/1‑141 (MQ=255)

            tGAGCGGATTAACAACTGAATTGTTGCTCTTAGCCGAATTAGATCATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAcgtcgt                                                                                                                      >  2:44706/1‑141 (MQ=255)

               gCGGATTAACAACTGAATTGTTGCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTaa                                                                                                                   >  1:152318/1‑141 (MQ=255)

                         aacTGAATTGTTTCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGc                                                                                                         <  1:103288/141‑1 (MQ=255)

                                   ttgCTCTTAGCCGAATTAGATAATCACCAACATTTATTATTCGATGACAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCCGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGaa                                                                                               >  2:254413/1‑141 (MQ=255)

                                         ttATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGaatcaatc                                                                                         >  1:302611/1‑141 (MQ=255)

                                                  ttAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTa                                                                                <  2:169977/141‑1 (MQ=255)

                                                    aGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAgg                                                                              <  1:24075/141‑1 (MQ=255)

                                                    aGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAgg                                                                              >  1:28634/1‑141 (MQ=255)

                                                       tAATCACCAACATTTATTATTCGATGATAAGAATCAAGTAAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGaaa                                                                           <  1:216378/141‑1 (MQ=255)

                                                       aaaTAACCAACATTAACTACTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGaaa                                                                           <  2:208394/140‑1 (MQ=255)

                                                              cAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAAGAAATACACGt                                                                    >  2:235014/1‑141 (MQ=255)

                                                              cAACATTTATTATTCGATGATAAGATTCAAGTAAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCCGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGt                                                                    >  2:197935/1‑141 (MQ=255)

                                                                     tattatTGCATGATAAGGATCAAGTCAATCAACTCATTAAAGATATCATTCGACATTAACAATTTGCTGCTGATGAAAAGTCGGTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTAc                                                             <  2:43990/141‑1 (MQ=255)

                                                                      attattCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCCGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACa                                                            <  2:296939/141‑1 (MQ=255)

                                                                        tattCGACGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATc                                                          <  2:350560/141‑1 (MQ=255)

                                                                         attCGAATAGAACATCCAAATCAATCAACACATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAACAGTCGTTAATCATTTTAGCTGACCTAGATTCAATCAATTTCCTAGGCAATCAACGTTTGTTACATct                                                         <  2:262170/141‑2 (MQ=255)

                                                                          ttCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCCGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCaa                                                        <  1:215789/141‑1 (MQ=255)

                                                                           tCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAg                                                       <  2:119508/141‑1 (MQ=255)

                                                                                   aaGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGt                                               >  2:386777/1‑141 (MQ=255)

                                                                                     gATTCCAGTCAACCAACTCACTAAAGATATCATCCCACATGAACAATTTGCCGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTaa                                             <  1:21412/141‑1 (MQ=255)

                                                                                        tCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCCGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTTGGAAATCAACGTTTGTTACATCAAGCATTGAGTAAttt                                          <  1:254413/141‑1 (MQ=255)

                                                                                          aaGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATttat                                        <  2:396310/141‑1 (MQ=255)

                                                                                           aGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGCATCAAGCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATttatt                                       >  1:388195/1‑141 (MQ=255)

                                                                                           aGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCTAGTGCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATttatt                                       >  1:89754/1‑141 (MQ=255)

                                                                                             tcaatcaaCTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCACGCATTGAGTAATTTATtaa                                     >  2:188793/1‑141 (MQ=255)

                                                                                             tcaatcaaCTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATTTATtaa                                     >  1:143656/1‑141 (MQ=255)

                                                                                                   aaCTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATTTATTAATAAATg                               >  1:61400/1‑141 (MQ=255)

                                                                                                               atatCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATTTATTAATAAATGCTATTAAGtata                   <  1:87433/141‑1 (MQ=255)

                                                                                                                tatCATTCGACATGAACAATTTGCCGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATTTATTAATAAATGCTATTAAGTATAc                  >  1:248393/1‑141 (MQ=255)

                                                                                                                     ttCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATTTATTAATAAATGCTATTAAGTATACAGAtt             >  2:352677/1‑140 (MQ=255)

                                                                                                                       cGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATTTATTAATAAATGCTATTAAGTATACAGATGtt           <  1:346616/141‑1 (MQ=255)

                                                                                                                                cAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATTTATTAATAAATGCTATTAAGTATACAGATGTTGGTGGTGcc  <  1:253895/141‑1 (MQ=255)

                                                                                                                                aaaTTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATTTATTAATAACTGCTATTAAGTATACAGATGTTGGTGGTGcc  <  1:207072/140‑1 (MQ=255)

TTACAACGCAGCTGAGCGGATTAACAACTGAATTGTTGCTCTTATCCGAATTAGATAATCACCAACATTTATTATTCGATGATAAGATTCAAGTCAATCAACTCATTAAAGATATCATTCGACATGAACAATTTGCTGCTGATGAAAAGTCGTTAATCATTTTAGCTGACCTAGAATCAATCAATTTCCTAGGAAATCAACGTTTGTTACATCAAGCATTGAGTAATTTATTAATAAATGCTATTAAGTATACAGATGTTGGTGGTGCC  >  USA300TCH1516_ALE/2482557‑2482825

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A