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 F52 I1 R1	27	78.9	1851050	96.3%	1782561	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,233,504	T→A	V470D (GTT→GAT)	prkC →	Serine/threonine‑protein kinase PrkC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,233,504	0	T	A	98.0%	165.3 / NA	51	V470D (GTT→GAT)	prkC	Serine/threonine‑protein kinase PrkC
Reads supporting (aligned to +/- strand): ref base T (0/1); major base A (21/28); minor base C (1/0); total (22/29)
Fisher's exact test for biased strand distribution p-value = 4.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAGTT  >  USA300TCH1516_ALE/1233370‑1233637

tGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGAt                                                                                                                                 <  1:847119/141‑1 (MQ=255)

ggAACGTGTTGGACGTGGTGACAGTGTTGATGTTGTTATATCAACTGGCCCTGAAAAGGGTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGAt                                                                                                                                 <  2:277363/140‑1 (MQ=255)

 gAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGAtt                                                                                                                                <  1:645242/141‑1 (MQ=255)

    cGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGaa                                                                                                                             <  2:108693/141‑1 (MQ=255)

      tgtTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGaaaa                                                                                                                           >  1:116097/1‑141 (MQ=255)

       gtTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGaaaaa                                                                                                                          <  2:341072/141‑1 (MQ=255)

       gtTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGaaaaa                                                                                                                          <  2:141411/141‑1 (MQ=255)

         tGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGt                                                                                                                        <  1:740525/141‑1 (MQ=255)

           aaCGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGtat                                                                                                                      <  1:109186/141‑1 (MQ=255)

                  ggACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATAtaataa                                                                                                               <  2:283893/140‑1 (MQ=255)

                    aCAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATGAAAAGCGTTAGGTCTTAAAGATGCTACGATTGAAAAAGTATATAATAATc                                                                                                             >  1:253558/1‑141 (MQ=255)

                       gtgtTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAACGGCGATGGTTTACCTTAGGAAGAAGCCTTGCAGAACTTAACATCGTGGGGTTTTAGAGATGAAATCATTGAAAAAGACTATAATCACCAAg                                                                                                          >  2:147373/1‑141 (MQ=255)

                        tgtTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAgc                                                                                                         <  1:35976/141‑1 (MQ=255)

                           tGATGTTGTTATCTCAGAGGGCCCTGAAAAGGTGAACATGCCAAGTGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATATTAATCAAGCGcc                                                                                                      <  2:816990/141‑1 (MQ=255)

                            gATGTTGTTATATCATAGGGCCCTGAAAAGGTTAAAATGACAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAAGTAAAATCGTTAGATCTTAAAAGTGATACGATTGAAAAAGTATATAAAAATCAAGCGCCa                                                                                                     >  2:888108/1‑141 (MQ=255)

                            gATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCa                                                                                                     >  2:251944/1‑141 (MQ=255)

                            gATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCa                                                                                                     >  1:739837/1‑141 (MQ=255)

                            gATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCa                                                                                                     >  1:851654/1‑141 (MQ=255)

                                      tatCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACa                                                                                           >  1:833262/1‑141 (MQ=255)

                                        tCAAAGGGCCCTGAAAAGGTTAACATGCCAAATGTCATTGGTTTACCTGAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACAtt                                                                                         >  2:24844/1‑141 (MQ=255)

                                        tCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGAGCCAAAAGGATACAtt                                                                                         >  2:316032/1‑141 (MQ=255)

                                           aaGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATACTCAAGCGCCAAAAGGATACATTGCa                                                                                      <  1:772478/141‑1 (MQ=255)

                                           aaGGGCCCTGAAAAGGTTAAAATGCCAAAGGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCa                                                                                      <  2:322309/141‑1 (MQ=255)

                                            aGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCaa                                                                                     >  2:677553/1‑141 (MQ=255)

                                            aGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCaa                                                                                     >  1:887511/1‑141 (MQ=255)

                                               gCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACGTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGAACTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATc                                                                                  <  2:320987/141‑1 (MQ=255)

                                                      aaaGGTTAAAAAGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAgtgt                                                                           <  1:634357/141‑1 (MQ=255)

                                                               aaTGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCaaa                                                                  >  1:411662/1‑141 (MQ=255)

                                                                  gCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATAc                                                               <  1:296114/141‑1 (MQ=255)

                                                                   ccAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACt                                                              >  2:273992/1‑141 (MQ=255)

                                                                    cAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATATGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTg                                                             <  1:608083/141‑1 (MQ=255)

                                                                    cAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTg                                                             >  1:484963/1‑141 (MQ=255)

                                                                    cAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGGAACCGCAAATACTg                                                             <  1:453011/141‑1 (MQ=255)

                                                                      aaTGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGaa                                                           >  1:382581/1‑141 (MQ=255)

                                                                       aTGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGaaa                                                          <  1:214751/141‑1 (MQ=255)

                                                                       aTGTCATTACTTGACCGAAGGAGGAAGCCTTGAAAAAAATAAAATCGCTAGGTCTTAAAGATGATCCGAATGAAAAAGTATATAAGAATCAATCGCCAAAAGGATACATTGCAAATCAAAGTGAAACCGCAAATACTGaaa                                                          <  1:319418/141‑1 (MQ=255)

                                                                         ttCATTGGTTTATCGAATGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAACGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATc                                                        <  2:390394/140‑1 (MQ=255)

                                                                              tGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTAt                                                   <  1:273992/141‑1 (MQ=255)

                                                                              tGGGTTACCTAAGCAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTAt                                                   <  1:274370/141‑1 (MQ=255)

                                                                                        aaGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGAAAAAAAAAAAAAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCt                                         <  2:574870/141‑1 (MQ=255)

                                                                                         aggaggAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTa                                        >  1:519820/1‑141 (MQ=255)

                                                                                         aggaggAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTa                                        >  2:64189/1‑141 (MQ=255)

                                                                                          ggaggaAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTaa                                       <  1:810290/141‑1 (MQ=255)

                                                                                           gaggaAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAGAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCCTGATTCTAat                                      >  1:881667/1‑141 (MQ=255)

                                                                                                 gCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTaaa                                >  1:571710/1‑141 (MQ=255)

                                                                                                 gCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTaaa                                >  1:571992/1‑141 (MQ=255)

                                                                                                    ttGCAGAAATTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAACGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAAGATTAAACta                             >  2:595713/1‑141 (MQ=255)

                                                                                                          aaaTTAAAATCGTTAGGTCTTAAAGATTATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGaa                       <  2:243760/141‑1 (MQ=255)

                                                                                                            aTTAAAATCGTTAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATc                     <  1:835020/141‑1 (MQ=255)

                                                                                                                      ttAGGTCTTAAAGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCAtt           <  2:850703/141‑1 (MQ=255)

                                                                                                                               aaaGATGATACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAGtt  <  2:808522/141‑1 (MQ=255)

TGAACGTGTTGAACGTGGTGACAGTGTTGATGTTGTTATATCAAAGGGCCCTGAAAAGGTTAAAATGCCAAATGTCATTGGTTTACCTAAGGAGGAAGCCTTGCAGAAATTAAAATCGTTAGGTCTTAAAGATGTTACGATTGAAAAAGTATATAATAATCAAGCGCCAAAAGGATACATTGCAAATCAAAGTGTAACCGCAAATACTGAAATCGCTATTCATGATTCTAATATTAAACTATATGAATCTTTAGGCATTAAGCAAGTT  >  USA300TCH1516_ALE/1233370‑1233637

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