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
A12 F1 I2 R1	69	53.0	2252012	96.1%	2164183	115.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,635,059	C→T	S263S (TCG→TCA)	stfQ ←	Qin prophage, putative side tail fibre assembly protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,635,059	0	C	T	100.0%	141.3 / NA	52	S263S (TCG→TCA)	stfQ	Qin prophage, putative side tail fibre assembly protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (23/29); total (23/29)

ACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCGGACAGCGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTCGTGTTCGTG  >  NC_000913/1634955‑1635194

aCGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTcc                                                                                                       <  1:830973/139‑1 (MQ=1)

 cGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTccc                                                                                                      <  2:1010781/139‑1 (MQ=11)

   gTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTg                                                                                                    <  2:182248/139‑1 (MQ=11)

             gtCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                          <  2:223609/139‑1 (MQ=14)

             gtCCATGAGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                          >  1:688343/1‑139 (MQ=14)

              tCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTc                                                                                         >  1:652235/1‑139 (MQ=14)

                   gtgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGcc                                                                                    >  2:438464/1‑139 (MQ=14)

                   gtgAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGcc                                                                                    >  1:39145/1‑139 (MQ=14)

                      aaCCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACt                                                                                 >  2:766918/1‑139 (MQ=17)

                        ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCa                                                                                   >  2:531510/1‑135 (MQ=17)

                        ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCa                                                                                   <  1:531510/135‑1 (MQ=17)

                        ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTAc                                                                               >  1:801708/1‑139 (MQ=17)

                        ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTAc                                                                               >  2:188345/1‑139 (MQ=17)

                        ccAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTAc                                                                               >  1:338522/1‑139 (MQ=17)

                           aTCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGc                                                                            <  2:801708/139‑1 (MQ=17)

                           aTCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGc                                                                            >  2:506635/1‑139 (MQ=17)

                                aaCGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgtt                                                                       >  2:910760/1‑139 (MQ=18)

                                 aCGGAGTGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                      <  1:506635/139‑1 (MQ=18)

                                       tGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTccc                                                                                                      >  2:24498/1‑101 (MQ=11)

                                       tGCGTATGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTccc                                                                                                      <  1:24498/101‑1 (MQ=11)

                                             tGAGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATcc                                                          <  1:1119088/139‑1 (MQ=21)

                                               aGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATcccc                                                        >  1:867853/1‑139 (MQ=21)

                                               aGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATcccc                                                        <  1:96699/139‑1 (MQ=21)

                                               aGCACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATcccc                                                        >  2:717717/1‑139 (MQ=21)

                                                 cACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                          >  1:35134/1‑103 (MQ=14)

                                                 cACCAATACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGt                                                                                          <  2:35134/103‑1 (MQ=14)

                                                      aTACCGACAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTa                                                 >  1:756894/1‑139 (MQ=25)

                                                            aCAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTg                                           >  2:936533/1‑139 (MQ=25)

                                                            aCAGTATGCGCGTGTGCACCTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTg                                           >  1:785031/1‑139 (MQ=25)

                                                                 atgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATc                                      <  1:766918/126‑1 (MQ=37)

                                                                 atgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATc                                      <  2:688343/126‑1 (MQ=37)

                                                                  tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  1:717717/127‑1 (MQ=37)

                                                                  tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  2:652235/127‑1 (MQ=37)

                                                                  tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  2:148410/127‑1 (MQ=37)

                                                                  tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  1:34229/127‑1 (MQ=37)

                                                                  tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  2:756894/127‑1 (MQ=37)

                                                                  tgcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcg                                     <  1:908875/127‑1 (MQ=37)

                                                                   gcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCt                                                   >  2:840780/12‑124 (MQ=25)

                                                                   gcgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCt                                                   <  1:840780/113‑1 (MQ=25)

                                                                    cgcgtgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATcgcg                                   <  2:982483/129‑1 (MQ=255)

                                                                        tgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                      <  2:198726/94‑1 (MQ=255)

                                                                        tgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                      >  1:198726/7‑100 (MQ=255)

                                                                        tgtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGtat                               <  1:789683/133‑1 (MQ=255)

                                                                        tgtgcaccTGCGCTTGCAGCAGAGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGtat                               <  2:148038/133‑1 (MQ=255)

                                                                         gtgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGtata                              <  1:188345/134‑1 (MQ=255)

                                                                          tgcaccTGCGCTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATaa                             >  1:529455/5‑139 (MQ=255)

                                                                                   gcTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAggg                    >  2:209678/1‑139 (MQ=255)

                                                                                    cTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                      >  2:162646/1‑88 (MQ=255)

                                                                                    cTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCttgttg                                                                      <  1:162646/88‑1 (MQ=255)

                                                                                    cTTGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGa                   <  1:936533/139‑1 (MQ=255)

                                                                                      tGCAGCAGTGCCGGACAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGaaa                 <  1:370374/139‑1 (MQ=255)

                                                                                                     cAGTGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTCGTGTTCGTg  <  2:39145/139‑1 (MQ=255)

ACGGTGATGGTGTGTCCATGTGAACCAATCGCAACGGAGTGCGTATGAGCACCAATACCGACAGTATGTGCATGCGCGCCTGCGCTTGCAGCAGTGCCGGACAGCGAGTGGGTATGAGCACCATCTGATGATGTCTTCCCTGCATTACGAGTCTGGCCACTACCGCTTGTTGTGCTCATAATCCCCGCGCTTAGATTTGAAATCGCGGTATAACCATTAGGGAAAATGCTCGTGTTCGTG  >  NC_000913/1634955‑1635194

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