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
A9 F174 I1 R1	26	63.3	1412239	95.2%	1344451	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,679,725	G→A	W70* (TGG→TAG)	ssaA2_4 →	Staphylococcal secretory antigen ssaA2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,679,725	0	G	A	77.6%	117.2 / 31.1	58	W70* (TGG→TAG)	ssaA2_4	Staphylococcal secretory antigen ssaA2
Reads supporting (aligned to +/- strand): ref base G (7/6); new base A (26/19); total (33/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

TCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAA  >  USA300TCH1516_ALE/2679588‑2679858

tCAATCCGTCGAACACACGCATCAATCGCATGCCGCAGTTAATTATTATAGTCAAAACCAATGTAAATGGTGGGAATTTAAACGTCGAGCACTAGTCGGTGAAACTATTTCTAATAGATGGCGCAATGCTAAAAATTGGTa                                                                                                                                    <  1:391543/141‑1 (MQ=255)

    tCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTAc                                                                                                                                >  1:959173/1‑141 (MQ=255)

      cGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACaa                                                                                                                              >  1:361227/1‑141 (MQ=255)

      cGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACaa                                                                                                                              >  1:911962/1‑141 (MQ=255)

      cGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACaa                                                                                                                              >  1:284944/1‑141 (MQ=255)

        tCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATg                                                                                                                            >  1:782843/1‑141 (MQ=255)

        tCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATg                                                                                                                            >  2:352923/1‑141 (MQ=255)

            aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACg                                                                                                                        <  1:461797/141‑1 (MQ=255)

            aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACg                                                                                                                        >  2:12305/1‑141 (MQ=255)

            aCAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACg                                                                                                                        <  1:298526/141‑1 (MQ=255)

              aaaCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTa                                                                                                                      <  1:179846/141‑1 (MQ=255)

                aCGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAAACAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTaaa                                                                                                                    >  1:515040/1‑141 (MQ=255)

                 cGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAAt                                                                                                                   >  1:896536/1‑141 (MQ=255)

                  gCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATc                                                                                                                  <  2:34437/141‑1 (MQ=255)

                    aTCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCaa                                                                                                                <  2:228773/141‑1 (MQ=255)

                         tCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAatat                                                                                                           >  2:46987/1‑141 (MQ=255)

                         tCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAatat                                                                                                           >  1:742383/1‑141 (MQ=255)

                         tCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAatat                                                                                                           <  2:65969/141‑1 (MQ=255)

                              tGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGAc                                                                                                      >  2:314855/1‑141 (MQ=255)

                                  gCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGt                                                                                                  >  1:416148/1‑141 (MQ=255)

                                  gCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGt                                                                                                  >  2:233955/1‑141 (MQ=255)

                                   cAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTc                                                                                                 <  1:914420/141‑1 (MQ=255)

                                            attatAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCaa                                                                                        <  1:277820/141‑1 (MQ=255)

                                                taGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGaaa                                                                                    <  1:535540/141‑1 (MQ=255)

                                                            aTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCAt                                                                        >  1:888870/1‑141 (MQ=255)

                                                            aTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCAt                                                                        >  1:854800/1‑141 (MQ=255)

                                                                aCATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCaa                                                                    >  1:468295/1‑141 (MQ=255)

                                                                aCATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCaa                                                                    <  1:704362/141‑1 (MQ=255)

                                                                   tggtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCa                                                                 >  1:546153/1‑141 (MQ=255)

                                                                   tggtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCa                                                                 <  2:327397/141‑1 (MQ=255)

                                                                   tggtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCa                                                                 >  2:91836/1‑141 (MQ=255)

                                                                     gtggGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAAc                                                               <  1:724431/141‑1 (MQ=255)

                                                                       gggCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTg                                                             >  1:505428/1‑141 (MQ=255)

                                                                        ggCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGc                                                            >  1:194659/1‑141 (MQ=255)

                                                                           aTTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAgg                                                         >  1:614727/1‑141 (MQ=255)

                                                                            tttAAACGGCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGa                                                        <  1:849268/141‑1 (MQ=255)

                                                                               aaaCGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGatat                                                     >  1:43894/1‑141 (MQ=255)

                                                                                  cGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGAtattat                                                  <  1:675545/141‑1 (MQ=255)

                                                                                   gTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATg                                                 <  1:795388/141‑1 (MQ=255)

                                                                                      gcgcACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGAc                                              >  1:890993/1‑141 (MQ=255)

                                                                                          acaAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGt                                          <  1:110025/141‑1 (MQ=255)

                                                                                             aGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGc                                       >  2:18108/1‑141 (MQ=255)

                                                                                                 ggTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAgtt                                   <  1:344977/141‑1 (MQ=255)

                                                                                                     aaCCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGttgttg                               <  1:119664/141‑1 (MQ=255)

                                                                                                     aaCCTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGttgttg                               <  1:19496/141‑1 (MQ=255)

                                                                                                       ccTGTTTCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGaa                             >  1:418631/1‑141 (MQ=255)

                                                                                                            ttCTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGt                        >  1:781735/1‑141 (MQ=255)

                                                                                                              cTAATAGATGGGGCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGtat                      <  1:856905/141‑1 (MQ=255)

                                                                                                                        gggCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACgg            <  1:198757/141‑1 (MQ=255)

                                                                                                                        gggCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACgg            >  1:629092/1‑141 (MQ=255)

                                                                                                                         ggCAATGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCCTGAAATCAACTGCAGGATATTATGGCCATGTCGCCATTGTTGAAAAAGTATATAAAAACGgt           >  2:335882/1‑141 (MQ=255)

                                                                                                                          gCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTTATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgta          >  1:741093/1‑141 (MQ=255)

                                                                                                                             aTGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgtagta       >  1:591840/1‑141 (MQ=255)

                                                                                                                             aTGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGgtagta       >  1:147579/1‑141 (MQ=255)

                                                                                                                              tGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTAt      <  2:41185/141‑1 (MQ=255)

                                                                                                                              tGCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTAt      <  1:14117/141‑1 (MQ=255)

                                                                                                                               gCTAAAAATTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTAtt     <  1:923624/141‑1 (MQ=255)

                                                                                                                                  aaaaaTTAGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTaaa  >  1:228413/1‑141 (MQ=255)

TCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAA  >  USA300TCH1516_ALE/2679588‑2679858

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `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