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
A3 F121 I0 R1	45	69.8	1582072	96.2%	1521953	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,744,443	C→A	59.3%	V77F (GTT→TTT)	apt ←	Adenine phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,744,443	0	C	A	59.3%	10.4 / 42.5	45	V77F (GTT→TTT)	apt	Adenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base C (5/13); new base A (15/11); total (20/25)
Fisher's exact test for biased strand distribution p-value = 6.85e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.21e-01

AGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTC  >  USA300TCH1516_ALE/1744303‑1744581

aGTAGCTAATAAAACATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                                                                                                                            <  2:618816/141‑1 (MQ=255)

         tacatcttcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTCCCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCaaa                                                                                                                                   <  1:253768/138‑1 (MQ=255)

           aaTCATCTGTACTTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGc                                                                                                                                 <  2:29936/141‑1 (MQ=255)

           aaTCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAACACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGc                                                                                                                                 >  1:475816/1‑141 (MQ=255)

                   gTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGCATGACTTCGCGAGGTAATTTCCCTTCTTTTCTAAAAGGTTCAAACACGATcccc                                                                                                                         >  2:18833/1‑141 (MQ=255)

                   gTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAAAGATTTTATTTGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATcccc                                                                                                                         <  1:615363/141‑1 (MQ=255)

                          acacacGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGaaa                                                                                                                  >  2:108255/1‑140 (MQ=255)

                          acacacGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAAt                                                                                                                  <  1:93836/141‑1 (MQ=255)

                           cacacGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCAATTGAATa                                                                                                                 >  1:253365/1‑141 (MQ=255)

                            acacGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATaa                                                                                                                >  1:190855/1‑141 (MQ=255)

                                 ttGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTAc                                                                                                           <  1:745407/141‑1 (MQ=255)

                                  tGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACa                                                                                                          >  1:461154/1‑141 (MQ=255)

                                   gACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAg                                                                                                         <  2:202012/141‑1 (MQ=255)

                                   gACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTACGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAGTCCCCATTGAATAAGCTACAg                                                                                                         >  1:103733/1‑141 (MQ=255)

                                    aCCTGGTTTAATTGGATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAgg                                                                                                        >  1:414526/1‑141 (MQ=255)

                                      cttgTTTAATTGCATCTTTGTGCATTTTTAAAACATTTGTACCATATTCTAGGTCATCCTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCCAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGAc                                                                                                      <  2:99404/138‑1 (MQ=255)

                                          tttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGcc                                                                                                  <  2:426664/141‑1 (MQ=255)

                                              aTTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATg                                                                                              <  1:76821/141‑1 (MQ=255)

                                               ttGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGa                                                                                             >  1:122534/1‑141 (MQ=255)

                                                tGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGTTGCAAAGCCAATACCCATTGAATAACCTACCGGTAAGCCAATGaa                                                                                            >  1:181202/1‑140 (MQ=255)

                                                tGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAACATCCCTACTTTTCTAACGGCTGCAAGGCCAATCCCCATTGAATAAGCTACAGGACAGCCAGTGAt                                                                                            >  2:675461/1‑141 (MQ=255)

                                                      tttGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGcc                                                                                      <  2:9847/141‑1 (MQ=255)

                                                            ctttGTTAAAACATTTTTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTACTTTCCTTTCTTTTCTAAAAGGTGCAAAGCCAATCTCCATTGAAGAAGCTACAGGACAGCCAATGATAAAGCCACgcgc                                                                                <  2:98866/139‑1 (MQ=255)

                                                             aTTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCt                                                                               <  2:37927/141‑1 (MQ=255)

                                                             aTTGTTAAAACATTTGTACCATACTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCt                                                                               <  2:6851/141‑1 (MQ=255)

                                                               tgtgAAAACATTTGTACCATATTCTAGGTCGTACTCATAACGAATGACTGCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTc                                                                             <  2:630859/141‑1 (MQ=255)

                                                                 ttAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAg                                                                           <  2:780618/141‑1 (MQ=255)

                                                                  tAAAACATTTGTACCATATTCTAGTTCATACTCATAACGAATGACTGCACGAGGTAATTTCCCTTCTTTTCTACAAGGTGCAAAGCCAATCCCCATTGAATAAGCGACAGGAAGGCCAATGATAAGGCGACGGGCtccgcg                                                                          >  1:171835/1‑136 (MQ=255)

                                                                  tAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTTATTTCCCTTCTTTTCTAAAAGGGGCAAAGCCAATCGCCATTGAGTAAGCGACAGGACAGGCAAAGATAAAGCCACGAGCttacgg                                                                          >  1:263179/1‑137 (MQ=255)

                                                                          ttGTTCCATATTCTAGGTCATACTCATAACGAATGACTTCACGATGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGACTAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACaa                                                                  <  2:21530/141‑1 (MQ=255)

                                                                             tACCATATTCTAGGTCATAAATCGAACGGAGGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGa                                                               >  1:782324/1‑141 (MQ=255)

                                                                               ccATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGata                                                             <  2:507034/141‑1 (MQ=255)

                                                                                          gTCATACTCATAACGAATGACTTCACGCGGTACTTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCCTTGAATAAGCTCCAGGACAGCCAATGATAAAGCCACGCCCTTCAGGTCCCACAACGATATCAACAtcccc                                                  >  2:168140/1‑138 (MQ=255)

                                                                                            cATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGt                                                >  1:322284/1‑141 (MQ=255)

                                                                                             aTACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTc                                               <  1:355883/141‑1 (MQ=255)

                                                                                               aCTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCtt                                             <  1:610597/141‑1 (MQ=255)

                                                                                                cTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCttt                                            >  1:603538/1‑141 (MQ=255)

                                                                                                  cATCACGAATGACTTCACGAGGTAATTTCCGTTCTTTTCTAAATGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTg                                          <  2:184048/141‑1 (MQ=255)

                                                                                                           tGACTTCACGAGGTAATTTCCCTTCTTTTCTACCAGGTGCAAAGCCAATCCCCATTGACTAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTa                                 <  2:518495/141‑1 (MQ=255)

                                                                                                                tCACGAGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGTGTATTCTACAAtt                            <  1:455395/141‑1 (MQ=255)

                                                                                                                     aGGTAATTTCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATc                       >  1:64255/1‑141 (MQ=255)

                                                                                                                         gaTTTCCCTTCTGTGCTACCAGCTGCAAAGCCAATCCNCATTGTATAAGCCACAGGACAGCCAATGATAGAGCCACGCGCTTCAGGTCCTACAACGAGATAAACCTCTCTGTCTTTTGCGTATTCTACAATTTTATCTGtt                   <  2:562164/140‑1 (MQ=255)

                                                                                                                           tttCCCTTCTTTTCTAAAAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTTTTGc                 >  2:227916/1‑141 (MQ=255)

                                                                                                                                  tcttTTCTAATAGGTGCAAAGCCGATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAGGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCa          <  2:290471/141‑1 (MQ=255)

                                                                                                                                    ttttCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCata        <  2:676215/141‑1 (MQ=255)

                                                                                                                                          aaCAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTc  >  1:718871/1‑141 (MQ=255)

AGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCGCTTCAGGTCCTACAACGATATCAACATCTCTGTCTTTTGCGTATTCTACAATTTTATCTGTTGCATAGCCATATGCTTC  >  USA300TCH1516_ALE/1744303‑1744581

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A