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 F44 I1 R1	56	64.5	2756482	98.4%	2712378	146.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947_CJ‑RC	4,741,362	C→T	intergenic (+492/+261)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	4,741,362	0	C	T	97.2%	113.9 / ‑4.4	36	intergenic (+492/+261)	gltA/yeiW	citrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (12/23); total (13/23)
Fisher's exact test for biased strand distribution p-value = 3.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

CGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAA‑CCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTC  >  NC_002947_CJ‑RC/4741231‑4741496

cGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCg                                                                                                                         <  4:18467/148‑1 (MQ=255)

  cctcctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCggac                                                                                                                      <  2:135611/149‑4 (MQ=255)

   ctcctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCggaca                                                                                                                     <  4:207105/149‑5 (MQ=255)

     cctTGATGGTCGTAATGTGAAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTAGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCggacac                                                                                                                    <  1:197502/148‑6 (MQ=255)

              tCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGtcctcctgc                                                                                                          <  8:330809/149‑4 (MQ=255)

                gTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGtcctcctgcag                                                                                                        >  3:272619/1‑144 (MQ=255)

                     gtgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcct                                                                                                   >  5:30240/1‑148 (MQ=255)

                          gcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctcgacc                                                                                              >  4:169755/1‑143 (MQ=255)

                           caCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctcgacct                                                                                             >  7:25458/1‑142 (MQ=255)

                           caCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGcgcctcgacct                                                                                             >  5:26841/1‑142 (MQ=255)

                                           gTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCtt                                                                             <  7:105444/149‑1 (MQ=255)

                                              aCCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGAt                                                                          <  5:221842/149‑1 (MQ=255)

                                                    cATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGt                                                                    <  5:241825/149‑1 (MQ=255)

                                                     aTGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTc                                                                   <  4:272619/149‑1 (MQ=255)

                                                      tGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTca                                                                  <  4:277352/149‑1 (MQ=255)

                                                             ttGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcgc                                                            <  7:312761/148‑1 (MQ=255)

                                                                 aCTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATa                                                        <  2:304737/148‑1 (MQ=255)

                                                                  cTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAgg                                                      >  6:112831/1‑149 (MQ=255)

                                                                     ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGc                                                     <  7:101164/147‑1 (MQ=255)

                                                                     ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCt                                                   >  2:340870/1‑149 (MQ=255)

                                                                      gTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCtt                                                  <  6:26841/149‑1 (MQ=255)

                                                                       tataGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTg                                                 <  5:290033/149‑1 (MQ=255)

                                                                         taGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTa                                               <  2:273403/149‑1 (MQ=255)

                                                                            gTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                                            >  8:124741/1‑149 (MQ=255)

                                                                            gTCCAGCACTGGACACCTTCGTGCATGAGCAGCTTCAGCGACATGC‑ATTCGTGAATCCAGGCACAGCCCCCCGACACGTCCTCCA‑GCAGCCCCTCGACCTTCGCCAGCGGCGCCTTGATCACGGACACACCGCGATACGCCAAGTACtt                                            >  2:217034/1‑149 (MQ=255)

                                                                             tCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTg                                           <  6:14673/149‑1 (MQ=255)

                                                                                aGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAc                                        <  3:329384/149‑1 (MQ=255)

                                                                                     tGGTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCg                                     <  3:126906/147‑1 (MQ=255)

                                                                                       gTCACCTTCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGc                                   <  7:303360/147‑1 (MQ=255)

                                                                                          aCCTTCGTGCTTGAT‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCt                              >  6:143707/1‑149 (MQ=255)

                                                                                             ttCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCt                              >  4:133043/1‑146 (MQ=255)

                                                                                             ttCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCt                              <  3:133043/146‑1 (MQ=255)

                                                                                             ttCGTGCTTGAG‑CAGCTTCTGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCACCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCAc                           >  7:172634/1‑149 (MQ=255)

                                                                                                                       ttgcaTTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATc          <  4:75740/137‑1 (MQ=255)

                                                                                                                       ttgcaTTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATc          >  3:75740/5‑141 (MQ=255)

                                                                                                                         gcaTTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCcgtcctc  <  4:174683/145‑1 (MQ=255)

CGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AACCTCCGCCAACTGCAATTCGTGAA‑CCAAGCAAAAGGCCCCGAAAAGGCCCTCC‑GCAGCCCCCCCAACCTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACTGAGGGACACCTTGATCCCGTCCTC  >  NC_002947_CJ‑RC/4741231‑4741496

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A