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 F75 I0 R1	16	35.0	795252	94.4%	750717	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,372,751	A→T	83.9%	L342* (TTA→TAA)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,372,751	0	A	T	83.9%	93.5 / 10.6	43	L342* (TTA→TAA)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand): ref base A (5/2); new base T (17/19); total (22/21)
Fisher's exact test for biased strand distribution p-value = 4.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

CTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAG  >  USA300TCH1516_ALE/2372617‑2372888

cTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGa                                                                                                                                     <  2:248379/141‑1 (MQ=255)

cTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGa                                                                                                                                     >  1:166121/1‑141 (MQ=255)

   gCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGAAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGTACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAaac                                                                                                                                  >  1:357323/1‑141 (MQ=255)

   gCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTCCACCCATTAATACACCTACCACCACTAAGGCTTGTCCAGAACCTTCACTCGTTACAACACCGATTACCGTACTAAATAACACCGCTTAtcgacaac                                                                                                                                  >  2:160517/1‑134 (MQ=255)

      atGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACGTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAaacaac                                                                                                                               <  1:369514/140‑1 (MQ=255)

       tGCAACTTTAAAGCTTTTTCAGTTGATCTCAGGAAAGTTTGCAGCCATTAATAACCCTATCGCCAGTAAGGCTGGTTTCGTAACTGCACTTGTTACAACAGCGATTAACGTACTAAAGAACAGCTCTTATAGGAaacaaca                                                                                                                              <  2:117727/141‑1 (MQ=255)

         cAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAaacaacaac                                                                                                                            >  2:212511/1‑141 (MQ=255)

         cAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAaacaacaac                                                                                                                            <  1:49333/141‑1 (MQ=255)

           aCTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCt                                                                                                                          <  1:109681/141‑1 (MQ=255)

            cttgtaaaCTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCAGTAATACACCTATCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGTTTATAGGAAACAACAACCTg                                                                                                                         <  2:104686/136‑1 (MQ=255)

            cTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTg                                                                                                                         <  1:144825/141‑1 (MQ=255)

            cTTCAAAACATTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTg                                                                                                                         <  1:215285/141‑1 (MQ=255)

              tCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGtt                                                                                                                       >  1:396510/1‑141 (MQ=255)

              tCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGtt                                                                                                                       >  1:277403/1‑141 (MQ=255)

              tCAAAACCTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACGAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGtt                                                                                                                       <  1:155590/141‑1 (MQ=255)

                aaaaCTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAATGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTAc                                                                                                                     <  1:331310/141‑1 (MQ=255)

                 aaaCTTTTCCAGTTTATCTCAGCAACGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATCGGAAACAACAACCTGTTACg                                                                                                                    >  2:221613/1‑141 (MQ=255)

                   aCTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAACCAACAACCTGTTACGAt                                                                                                                  >  1:376998/1‑141 (MQ=255)

                            gTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCaaa                                                                                                         >  1:120578/1‑141 (MQ=255)

                              ttATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTCGCAAATc                                                                                                       >  1:287390/1‑141 (MQ=255)

                                   tcatcaAAGTTTGCAGCCATTAATACACCTACCACCACTAAGTCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACACCGCTTATCGGAAACAACAACCTGTTACGCTACTAGCAAATCCTGtt                                                                                                  <  2:306011/141‑1 (MQ=255)

                                     aGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGACACAACAACCTGTTACGATACTAGCAAATCCTGTTCt                                                                                                >  1:156114/1‑141 (MQ=255)

                                         aaacttGCTGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTATTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAAAAACAACCTGTTACGATACTACCAAATCCTGTTCTATCa                                                                                            >  2:51077/5‑141 (MQ=255)

                                          aGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCAc                                                                                           <  1:196859/141‑1 (MQ=255)

                                              tgaaGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACGTGGTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTATAGCACCTAc                                                                                       >  1:144799/4‑141 (MQ=255)

                                              tGCAGCCATTAATACACCGACCACCAATAAGGCTGGTGTCGTAACTGCACTTGTTACAACGGCGATTACCGGACTAAAGAACGGCGCTTATAGGAAACAACAACCTATTACGATACTAGCAAATCCTGTTCTAGCACCTAc                                                                                       >  1:284432/1‑141 (MQ=255)

                                                cAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCATTATCAAGCACCTAcca                                                                                     >  2:233240/1‑139 (MQ=255)

                                                                     ccaccaAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTTCCGGAGTAAAGAACAGCGCTTATAGGAAACAACAACCTGTGACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGa                                                                <  2:83212/141‑1 (MQ=255)

                                                                      cacTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGat                                                               >  1:75949/1‑141 (MQ=255)

                                                                       acTAAGGCTGGTGTCGTAACTGCACTGAGTAAAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGata                                                              <  1:12261/141‑1 (MQ=255)

                                                                        cTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGatat                                                             >  2:252417/1‑141 (MQ=255)

                                                                                  tcttgTAACTGCACTTGGTACAACAGGGATTAACGCACTAATGAACAGTGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAgttgt                                                   <  2:3152/137‑1 (MQ=255)

                                                                                    tCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGttgttg                                                 <  1:118155/141‑1 (MQ=255)

                                                                                    ccGTAAGTGCACTTGTTACAACAGCGAGTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTGGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGttgttg                                                 <  2:89751/140‑1 (MQ=255)

                                                                                       tAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAg                                              >  1:260433/1‑141 (MQ=255)

                                                                                                 tgctACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCaaa                                    <  1:84583/138‑1 (MQ=255)

                                                                                                 tGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCCAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCaaa                                    <  1:212511/141‑1 (MQ=255)

                                                                                                           gCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCt                          <  1:212111/141‑1 (MQ=255)

                                                                                                                       caaaaGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCt              <  1:104911/139‑1 (MQ=255)

                                                                                                                            gAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGAACCTACAGCAACACCTGAAGTTGATTCGATATAAGACGTTGTTGTAGTTGTTCCAAAACTTGATCCTACAATCGTAGATaaaag         >  2:331797/1‑139 (MQ=255)

                                                                                                                              aCAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATGCTACAATCGTAGCTAAAGAAt       >  1:234204/1‑141 (MQ=255)

                                                                                                                                  agcTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGATCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAACAATCTga   >  2:108310/2‑141 (MQ=255)

                                                                                                                                   gcTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGACGTTGTTGTAGTCGGTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTgac  >  2:177673/1‑140 (MQ=255)

CTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGAG  >  USA300TCH1516_ALE/2372617‑2372888

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