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
A7 F28 I1 R1	172	67.8	2301510	98.9%	2276193	138.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,577,067	(C)_6→7	coding (892/1047 nt)	mcrC ←	5‑methylcytosine‑specific restriction enzyme subunit McrC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,577,061	1	.	C	94.9%	124.7 / 0.1	39	coding (898/1047 nt)	mcrC	5‑methylcytosine‑specific restriction enzyme subunit McrC
Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (23/14); total (24/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01

ATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAA‑‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGCTCTTATAGTATTTGGCGTC  >  NC_000913/4576923‑4577190

atTCATCGAAAATGTCGAGAAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAA‑‑c                                                                                                                                  >  2:43461/1‑140 (MQ=255)

 ttCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAA‑‑cc                                                                                                                                 >  2:287781/1‑140 (MQ=255)

 ttCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAA‑‑cc                                                                                                                                 <  2:198962/140‑1 (MQ=255)

       gAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAA‑‑ccccccct                                                                                                                           <  2:734176/140‑3 (MQ=255)

            tGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGtt                                                                                                                       >  1:234275/1‑140 (MQ=255)

                       tCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCAtttt                                                                                                            <  2:561151/140‑1 (MQ=255)

                                 taCACGGCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCAtttt                                                                                                            >  1:96791/1‑130 (MQ=255)

                                 taCACGGCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCAtttt                                                                                                            <  2:96791/130‑1 (MQ=255)

                                      ggCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTaa                                                                                                  >  1:132208/1‑135 (MQ=255)

                                      ggCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTaa                                                                                                  <  2:132208/135‑1 (MQ=255)

                                             ccTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAACCCCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGt                                                                                       <  1:288876/140‑1 (MQ=255)

                                                     aaaTTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATtcatca                                                                              <  2:645405/140‑1 (MQ=255)

                                                             ggTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAA‑‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATaaa                                                                     >  1:612261/1‑140 (MQ=255)

                                                                acacAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGa                                                                   >  1:255492/1‑140 (MQ=255)

                                                                      gCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGc                                                             >  1:1146651/1‑140 (MQ=255)

                                                                           tatCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATg                                                        >  1:583393/1‑140 (MQ=255)

                                                                              cGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGaaa                                                     >  1:267349/1‑140 (MQ=255)

                                                                                aaGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAAtt                                                   >  2:236945/1‑140 (MQ=255)

                                                                                aaGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAAtt                                                   >  2:903481/1‑140 (MQ=255)

                                                                                aaGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAAtt                                                   >  1:581277/1‑140 (MQ=255)

                                                                                   ccATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAAttttt                                                <  1:236945/140‑1 (MQ=255)

                                                                                   ccATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAA‑‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTc                                               <  1:5970/140‑1 (MQ=255)

                                                                                      ttAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTg                                             <  2:581277/140‑1 (MQ=255)

                                                                                               taACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACGATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATtc                                    >  1:18405/1‑140 (MQ=255)

                                                                                               taACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATtc                                    >  2:634942/1‑140 (MQ=255)

                                                                                                    aTGTTTCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATGTTTCTGTTCCCATTcgtcgt                               >  1:780299/1‑140 (MQ=255)

                                                                                                       tttCACTGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGaa                            >  2:616995/1‑140 (MQ=255)

                                                                                                             tGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATg                      <  1:903481/140‑1 (MQ=255)

                                                                                                             tGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATg                      <  1:472481/140‑1 (MQ=255)

                                                                                                             tGCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATg                      <  1:616995/140‑1 (MQ=255)

                                                                                                              gCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGc                     <  1:634942/140‑1 (MQ=255)

                                                                                                              gCGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGc                     <  2:583393/140‑1 (MQ=255)

                                                                                                               cGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGaaaaaa                        <  1:1130837/136‑1 (MQ=255)

                                                                                                               cGGTATCTACGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGaaaaaa                        >  2:1130837/1‑136 (MQ=255)

                                                                                                                       aCGTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAGGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGCTCTTATAGt            >  2:1024431/1‑140 (MQ=255)

                                                                                                                         gTGGGGATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGCTCTTATAGTAt          >  2:890290/1‑140 (MQ=255)

                                                                                                                           ggggATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGCTCTTATAGTAttt        >  1:1051381/1‑140 (MQ=255)

                                                                                                                            gggATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGCTCTTATAGTATTTg       >  1:651210/1‑140 (MQ=255)

                                                                                                                              gATATATTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGCTCTTATAGTATTTGGc     >  2:85416/1‑140 (MQ=255)

                                                                                                                                tatatTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGctc                   >  2:394798/1‑124 (MQ=255)

                                                                                                                                tatatTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGctc                   <  1:394798/124‑1 (MQ=255)

                                                                                                                                tatatTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGCTCTTATAGTATTTGGCGt   >  2:693277/1‑140 (MQ=255)

                                                                                                                                 atatTAATAAC‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGCTCTTATAGTATTTGGCGTc  >  2:875437/1‑140 (MQ=255)

ATTCATCGAAAATGTCGAGTAATTCTTGATGTATACACGGCCATTCCTGACCTAAATTGACGGTACACAAGCCAATATCGAAGCCATTAATTTTATAACGATGTTTCACTGCGGTATCTACGTGGGGATATATTAATAA‑‑CCCCCCTATGTTTTCGCCATTTTCAGGCTTTAACGACCATAAGTAATTCATCAGTTGATAAAGATTTTGCGAATGAAATTTTTCTGTTCCCATTCGTCGTGAAAAAATGCTCTTATAGTATTTGGCGTC  >  NC_000913/4576923‑4577190

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A