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
A4 F1 I1 R1	73	24.7	1166784	93.9%	1095610	107.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,071,500	A→G	noncoding (184/195 nt)	isrC →	novel sRNA, CP4‑44, putative prophage remnant

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,071,500	0	A	G	100.0%	122.7 / NA	33	noncoding (184/195 nt)	isrC	novel sRNA, CP4‑44, putative prophage remnant
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/17); total (16/17)

CCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAA  >  NC_000913/2071369‑2071633

ccTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCtt                                                                                                                                >  2:43151/1‑139 (MQ=255)

    tGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCtttttt                                                                                                                            >  2:99035/1‑139 (MQ=255)

    tGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCtttttt                                                                                                                            >  2:316740/1‑139 (MQ=255)

    tGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCtttttt                                                                                                                            >  1:170288/1‑139 (MQ=255)

     gTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTa                                                                                                                           >  2:243281/1‑139 (MQ=255)

     gTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTa                                                                                                                           >  1:402744/1‑139 (MQ=255)

       cAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTAtt                                                                                                                         <  1:43151/139‑1 (MQ=255)

       cAGAAACATGCACAAATACGTACAGAAAGACATTCAGGGAACAACAGACCCACATTTCAGAAACCCCCACAGCGGGACCCCCGGCATTGTAACCCTTTCCCTGCCGGTATCCACGTTTGGGGGGGCCGGTTTTTTTAtc                                                                                                                         <  1:294826/139‑2 (MQ=255)

                      aTACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAg                                                                                                          >  1:550878/1‑139 (MQ=255)

                                       ttCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACg                                                                                         <  1:316740/139‑1 (MQ=255)

                                        tCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTAtt                                                                                                                         >  1:220939/1‑106 (MQ=255)

                                        tCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTAtt                                                                                                                         <  2:220939/106‑1 (MQ=255)

                                          aGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACa                                                                                      >  2:114007/1‑139 (MQ=255)

                                               acaacaGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGa                                                                                 <  1:99035/139‑1 (MQ=255)

                                               acaacaGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGa                                                                                 <  2:170288/139‑1 (MQ=255)

                                                   caGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATAc                                                                             <  1:114007/139‑1 (MQ=255)

                                                      aaCCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   <  1:36289/98‑1 (MQ=255)

                                                      aaCCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   >  2:36289/1‑98 (MQ=255)

                                                                cAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTg                                                                >  1:127070/1‑139 (MQ=255)

                                                                     aCTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATg                                                           <  1:31665/139‑1 (MQ=255)

                                                                       tCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGa                                                         <  2:402744/139‑1 (MQ=255)

                                                                                         ggCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   <  2:58638/63‑1 (MQ=255)

                                                                                         ggCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   >  1:58638/1‑63 (MQ=255)

                                                                                         ggCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCtt                                       <  1:243281/139‑1 (MQ=255)

                                                                                             cTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   >  1:547366/1‑59 (MQ=255)

                                                                                             cTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCt                                                                                                                   <  2:547366/59‑1 (MQ=255)

                                                                                              tGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATc                                                                                    <  2:400523/89‑1 (MQ=255)

                                                                                              tGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATc                                                                                    >  1:400523/1‑89 (MQ=255)

                                                                                                tAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGa                                                                                        >  2:286025/1‑83 (MQ=255)

                                                                                                tAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGa                                                                                        <  1:286025/83‑1 (MQ=255)

                                                                                                                  tATCCACGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCcg              <  2:550878/139‑1 (MQ=255)

                                                                                                                       aCGTTTGTGGGTGCCGGCTTTTTTATTCACCCTCAGTCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCAc         <  2:82991/139‑1 (MQ=255)

                                                                                                                              tgGGTGCCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTaa  >  1:126455/1‑139 (MQ=255)

CCTTTGTCAGTAACATGCACAGATACGTACAGAAAGACATTCAGGGAACAACAGAACCACAATTCAGAAACTCCCACAGCCGGACCTCCGGCACTGTAACCCTTTACCTGCCGGTATCCACGTTTGTGGGTACCGGCTTTTTTATTCACCCTCAATCTAAGGAAAAGCTGATGAAACGACATCTGAATACCTGCTACAGGCTGGTATGGAATCACATGACGGGCGCTTTCGTGGTTGCCTCCGAACTGGCCCGCGCACGGGGTAA  >  NC_000913/2071369‑2071633

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A