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 F169 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,440,085	G→T	intergenic (‑45/+126)	cspA_2 ← / ← USA300TCH1516_01338	Cold shock protein CspA/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,440,085	0	G	T	96.4%	90.6 / NA	29	intergenic (‑45/+126)	cspA_2/USA300TCH1516_01338	Cold shock protein CspA/hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (0/0); major base T (11/16); minor base C (1/0); total (12/17)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTAG  >  USA300TCH1516_ALE/1439940‑1440228

ttAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCa                                                                                                                                               >  4:216611/1‑148 (MQ=255)

     tGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAAACTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTa                                                                                                                                          >  4:6862/1‑148 (MQ=255)

         gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaa                                                                                                                                      >  3:89538/1‑148 (MQ=255)

            aaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaaa                                                                                                                                   <  4:62511/148‑1 (MQ=255)

                gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaa                                                                                                                                      >  1:20205/1‑141 (MQ=255)

                  aCGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATg                                                                                                                             <  3:175702/148‑1 (MQ=255)

                         cGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCCTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAttt                                                                                                                      <  4:209095/148‑1 (MQ=255)

                           tCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCa                                                                                                                    <  4:301789/148‑1 (MQ=255)

                            cATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCAc                                                                                                                   >  3:34671/1‑148 (MQ=255)

                            cATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGAACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCCCATATTACAAAAAATACATGCAAATTTCAc                                                                                                                   >  3:211701/1‑148 (MQ=255)

                                              cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                        <  1:34209/141‑1 (MQ=255)

                                                aTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCACGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                                                                               <  4:305585/148‑1 (MQ=255)

                                                aTAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGAATAAAATTCATTCAATATGCTTATAAAAAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                                                                               <  4:146575/148‑1 (MQ=255)

                                                 tAAAGCCGAATCCTTTTTCCGCGTACGGCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTg                                                                                                     <  2:65787/141‑1 (MQ=255)

                                                               ttttCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataat                                                                                       <  2:59778/141‑1 (MQ=255)

                                                                   cAGCGTTAAACCATTTAACTGTACCATATTTCATAATCTGAAACCTCCAAGACTAAAATTCATGCAATATGCTTATTATAATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTaa                                                                            <  4:113389/148‑1 (MQ=255)

                                                                      cGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACtt                                                                         >  4:10042/1‑148 (MQ=255)

                                                                        ttAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGt                                                                       >  4:357101/1‑148 (MQ=255)

                                                                               aTTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAg                                                                >  3:170754/1‑148 (MQ=255)

                                                                                tttAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGta                                                                      <  1:42306/141‑1 (MQ=255)

                                                                                        tACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttat                                                       <  3:216611/148‑1 (MQ=255)

                                                                                             tGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCa                                                  >  3:42183/1‑148 (MQ=255)

                                                                                             tGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTGATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCa                                                  >  3:11469/1‑148 (MQ=255)

                                                                                                 tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAtt                                              <  3:121695/148‑1 (MQ=255)

                                                                                                      aTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGTAGTTATTACCAAATTGcaat                                         <  3:179491/148‑1 (MQ=255)

                                                                                                      aTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaat                                         <  3:370350/148‑1 (MQ=255)

                                                                                                           aaaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaat                                    >  4:147577/1‑148 (MQ=255)

                                                                                                                               cattcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTaa                <  4:15915/148‑1 (MQ=255)

                                                                                                                                             aTTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTAg  <  3:313149/148‑1 (MQ=255)

TTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTAG  >  USA300TCH1516_ALE/1439940‑1440228

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A