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 F104 I0 R1	54	57.6	1336546	96.4%	1288430	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	129,796	G→C	92.5%	intergenic (‑209/+212)	spa ← / ← sarS	Immunoglobulin G‑binding protein A/HTH‑type transcriptional regulator SarS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	129,796	0	G	C	92.5%	168.9 / 6.5	54	intergenic (‑209/+212)	spa/sarS	Immunoglobulin G‑binding protein A/HTH‑type transcriptional regulator SarS
Reads supporting (aligned to +/- strand): ref base G (2/2); new base C (17/32); total (19/35)
Fisher's exact test for biased strand distribution p-value = 6.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.35e-01

TATTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGAGATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAGTTGTT  >  USA300TCH1516_ALE/129660‑129928

tatTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATCAAATATAGACatat                                                                                                                                  >  2:623762/1‑141 (MQ=255)

 atTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATAtt                                                                                                                                 <  2:85801/141‑1 (MQ=255)

 atTTATAATTAAAATTAAAGGTAAGTTTCTCTACTTATAAAATAACCATTTCCCGAAAATATGTATTCACAAAAAAAAAGACTGAAAACCTCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATAtt                                                                                                                                 <  2:58037/141‑1 (MQ=255)

           aaaTTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATg                                                                                                                       <  1:44741/141‑1 (MQ=255)

           aaaTTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATg                                                                                                                       >  2:50496/1‑141 (MQ=255)

                   aGGTAAGGTTTACAACTTATAAAAAAAAGATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGAGATATTTTTTATAATGAAAGCGGt                                                                                                               <  2:328942/141‑1 (MQ=255)

                       aaGTTTTACAACTTATAAAATAAATATTGTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTaa                                                                                                           >  1:428873/1‑141 (MQ=255)

                        aGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAAT‑AAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATa                                                                                                         <  1:528078/141‑1 (MQ=255)

                          tgttACTACCTATAAAATAAATACTTTGCAGAAAGATTTATTCAGGAAGGAAAAGGCTTAAAACCGAAAAATCACGATATTTCGAGTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATAc                                                                                                        <  1:54642/139‑1 (MQ=255)

                             tACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACata                                                                                                     <  2:109866/141‑1 (MQ=255)

                              aCAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACatat                                                                                                    >  2:438285/1‑141 (MQ=255)

                                aaCTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGa                                                                                                  <  1:164024/141‑1 (MQ=255)

                                 aCTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAg                                                                                                 >  1:315106/1‑141 (MQ=255)

                                  cTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGt                                                                                                <  2:78411/141‑1 (MQ=255)

                                  attATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGt                                                                                                <  1:210834/140‑1 (MQ=255)

                                   ttATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATCTTTGTTAAATTAAAAGCGGTTTCCTACATATGAGtt                                                                                               >  2:166994/1‑141 (MQ=255)

                                   ttATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGtt                                                                                               >  1:506397/1‑141 (MQ=255)

                                     ataaaataaaTATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGAGATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTaa                                                                                             >  2:525412/1‑141 (MQ=255)

                                        aaataaatATGTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAACCCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTaaaaa                                                                                          <  1:590494/141‑1 (MQ=255)

                                         aataaataTTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTATAATACATATGAGTTaaaaaa                                                                                         >  2:221659/1‑141 (MQ=255)

                                                   ttGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACTCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAg                                                                               <  2:435925/141‑1 (MQ=255)

                                                   ttGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAg                                                                               <  1:502094/141‑1 (MQ=255)

                                                   ttGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTCTAATACCTCTGAGCTAAAAAATATTTTTAAg                                                                               <  2:660171/141‑1 (MQ=255)

                                                       tGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAACAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGGGTTAAAAAATATTTTCAAGAATa                                                                           >  2:1129/1‑141 (MQ=255)

                                                       tGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATa                                                                           <  1:283936/141‑1 (MQ=255)

                                                       tGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATa                                                                           <  1:114449/141‑1 (MQ=255)

                                                            gATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTg                                                                      >  1:270445/1‑141 (MQ=255)

                                                              tttATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTggg                                                                    <  1:50496/141‑1 (MQ=255)

                                                                  ttCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCtt                                                                <  1:508097/141‑1 (MQ=255)

                                                                       gAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCAGTTTAATACATATGAGTTAAAAAATATTTTTAAGCATAAAGTGGGGCTTTGAAt                                                           <  1:432429/141‑1 (MQ=255)

                                                                          gTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAAtgtg                                                        >  1:4706/1‑141 (MQ=255)

                                                                              aaGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGGTTAATACATATGAGATAAAAAATATTTTTAAGAATACAGTGAGGCTTTGAATGTGCTGa                                                    >  2:285595/1‑141 (MQ=255)

                                                                                gtcctAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAgg                                                  <  1:311248/137‑1 (MQ=255)

                                                                                ggCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAgg                                                  <  1:309796/141‑1 (MQ=255)

                                                                                  cTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGCAATCAATGTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGtt                                                <  1:316120/141‑1 (MQ=255)

                                                                                  cTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTGGAATGTGCTGAGGtt                                                <  1:495072/141‑1 (MQ=255)

                                                                                  cTTAAAACCGCAAAAACACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGtt                                                <  1:64463/141‑1 (MQ=255)

                                                                                   ttAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGttt                                               <  2:636788/141‑1 (MQ=255)

                                                                                   ttAAAACCGCAAAATCACGCCATTTCTATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGttt                                               <  1:270169/141‑1 (MQ=255)

                                                                                      aaaCCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTTTAATGAAAGCGGGTTAATACATATGAGTTAAAAAATATTTTTAAGAATAATGTGGGGCTTTGAATATGCTGAGGTTTact                                            >  1:81195/1‑139 (MQ=255)

                                                                                          ccaaaaaTCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCg                                        <  2:327648/138‑1 (MQ=255)

                                                                                          cGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCg                                        <  2:58949/141‑1 (MQ=255)

                                                                                            cAAAAGCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGCGGTTTGAATGTGCTGAGGTTTAATTTCGGa                                      <  1:489464/141‑1 (MQ=255)

                                                                                               aaTCACGCTATTTCGATTAATAAAAACAGATAAAATATAGAGATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAAt                                   <  1:525412/141‑1 (MQ=255)

                                                                                               aaTCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAAt                                   >  1:548932/1‑141 (MQ=255)

                                                                                                aTCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTTTATTTTTAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATg                                  >  2:653433/1‑141 (MQ=255)

                                                                                                 tCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATgg                                 <  2:614669/141‑1 (MQ=255)

                                                                                                 tCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATAGTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATgg                                 <  2:193788/141‑1 (MQ=255)

                                                                                                           tCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGa                       <  1:646347/141‑1 (MQ=255)

                                                                                                           tCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGa                       <  1:610468/141‑1 (MQ=255)

                                                                                                                taataaAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATatag                  <  1:438285/141‑1 (MQ=255)

                                                                                                                    aaaaaCAGATAAAATATAGAGATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATATCGGAAATGGTTTTAAGTGATatagaaaa              >  2:47376/1‑141 (MQ=255)

                                                                                                                            aTAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgt      >  1:396630/1‑141 (MQ=255)

                                                                                                                                aaTATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgtt  >  1:132235/1‑141 (MQ=255)

TATTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGAGATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAGTTGTT  >  USA300TCH1516_ALE/129660‑129928

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